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Built site for AMR: 2.0.0.9005@147f911
This commit is contained in:
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@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -187,7 +187,7 @@
|
||||
website update since they are based on randomly created values and the
|
||||
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
|
||||
Markdown</a>. However, the methodology remains unchanged. This page was
|
||||
generated on 20 March 2023.</p>
|
||||
generated on 14 April 2023.</p>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2023-03-20</td>
|
||||
<td align="center">2023-04-14</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2023-03-20</td>
|
||||
<td align="center">2023-04-14</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2023-03-20</td>
|
||||
<td align="center">2023-04-14</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -300,7 +300,7 @@ have extracted from their laboratory systems:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 E. coli R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 E. coli S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 S. aureus S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,990 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># we will use 'our_data' as the data set name for this tutorial</span></span>
|
||||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">example_isolates_unclean</span></span></code></pre></div>
|
||||
@ -449,7 +449,7 @@ dplyr:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 B_ESCHR_COLI R S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,990 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
|
||||
<p>This is basically it for the cleaning, time to start the data
|
||||
inclusion.</p>
|
||||
</div>
|
||||
@ -532,7 +532,7 @@ like:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,616 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span></code></pre></div>
|
||||
<p>Time for the analysis.</p>
|
||||
</div>
|
||||
</div>
|
||||
@ -635,7 +635,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@ -654,7 +654,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@ -671,7 +671,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> B_STPHY_AURS S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 2,616 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,616 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
@ -690,7 +690,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 961 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 961 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
|
||||
@ -709,7 +709,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> W9 A 2013-10-02 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 461 more rows</span></span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 461 more rows</span></span></span>
|
||||
<span></span>
|
||||
<span><span class="co"># even works in base R (since R 3.0):</span></span>
|
||||
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
|
||||
@ -728,7 +728,7 @@ in:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> W9 A 2013-10-02 B_ESCHR_COLI R R S S TRUE </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 461 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 461 more rows</span></span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
|
||||
@ -962,110 +962,110 @@ antibiograms:</p>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (410-410)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">62</td>
|
||||
<em>E. coli</em> (453-453)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">66</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (430-430)</td>
|
||||
<em>E. coli</em> (387-387)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>E. coli</em> (410-410)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (96-96)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">45</td>
|
||||
<td align="right">57</td>
|
||||
<em>K. pneumoniae</em> (113-113)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">48</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">58</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (108-108)</td>
|
||||
<td align="right">68</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>K. pneumoniae</em> (112-112)</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">50</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">58</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (220-220)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">63</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (198-198)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">52</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">65</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (243-243)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (124-124)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">63</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (141-141)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">52</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">56</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (134-134)</td>
|
||||
<td align="right">67</td>
|
||||
<td align="right">60</td>
|
||||
<em>K. pneumoniae</em> (91-91)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">68</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (212-212)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">53</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">69</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (234-234)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">66</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. aureus</em> (215-215)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">61</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (140-140)</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (139-139)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">68</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">
|
||||
<em>S. pneumoniae</em> (120-120)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">68</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1090,44 +1090,44 @@ antibiograms:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-negative (506-506)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">55</td>
|
||||
<td align="right">62</td>
|
||||
<td align="left">Gram-negative (566-566)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">57</td>
|
||||
<td align="right">65</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-negative (538-538)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="left">Gram-negative (499-499)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">60</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-negative (522-522)</td>
|
||||
<td align="left">Gram-negative (501-501)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">58</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">62</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-positive (344-344)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">59</td>
|
||||
<td align="right">63</td>
|
||||
<td align="left">Gram-positive (352-352)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">54</td>
|
||||
<td align="right">61</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-positive (339-339)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">52</td>
|
||||
<td align="right">65</td>
|
||||
<td align="left">Gram-positive (373-373)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">56</td>
|
||||
<td align="right">67</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-positive (377-377)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">58</td>
|
||||
<td align="left">Gram-positive (335-335)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">60</td>
|
||||
<td align="right">64</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -1152,45 +1152,45 @@ antibiograms:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-negative (506-506)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="left">Gram-negative (566-566)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">74</td>
|
||||
<td align="right">78</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-negative (538-538)</td>
|
||||
<td align="right">65</td>
|
||||
<td align="right">78</td>
|
||||
<td align="left">Gram-negative (499-499)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">77</td>
|
||||
<td align="right">72</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-negative (522-522)</td>
|
||||
<td align="left">Gram-negative (501-501)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">74</td>
|
||||
<td align="right">73</td>
|
||||
<td align="right">74</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Cardial</td>
|
||||
<td align="left">Gram-positive (344-344)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="right">75</td>
|
||||
<td align="left">Gram-positive (352-352)</td>
|
||||
<td align="right">62</td>
|
||||
<td align="right">75</td>
|
||||
<td align="right">73</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Respiratory</td>
|
||||
<td align="left">Gram-positive (339-339)</td>
|
||||
<td align="right">63</td>
|
||||
<td align="left">Gram-positive (373-373)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">80</td>
|
||||
<td align="right">77</td>
|
||||
<td align="right">74</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Rheumatic</td>
|
||||
<td align="left">Gram-positive (377-377)</td>
|
||||
<td align="right">66</td>
|
||||
<td align="right">79</td>
|
||||
<td align="right">77</td>
|
||||
<td align="left">Gram-positive (335-335)</td>
|
||||
<td align="right">64</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">76</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 42 KiB After Width: | Height: | Size: 42 KiB |
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co">#> 1 I R I I S R</span></span>
|
||||
<span><span class="co">#> 2 I R R S S I</span></span>
|
||||
<span><span class="co">#> 3 I R S R R R</span></span>
|
||||
<span><span class="co">#> 4 R R I R I R</span></span>
|
||||
<span><span class="co">#> 5 R R R R R S</span></span>
|
||||
<span><span class="co">#> 6 S R S S R S</span></span>
|
||||
<span><span class="co">#> 1 I I I R S S</span></span>
|
||||
<span><span class="co">#> 2 S R R R R S</span></span>
|
||||
<span><span class="co">#> 3 I R S I I S</span></span>
|
||||
<span><span class="co">#> 4 I S S S S R</span></span>
|
||||
<span><span class="co">#> 5 S I R I R R</span></span>
|
||||
<span><span class="co">#> 6 S I I I I R</span></span>
|
||||
<span><span class="co">#> kanamycin</span></span>
|
||||
<span><span class="co">#> 1 I</span></span>
|
||||
<span><span class="co">#> 2 I</span></span>
|
||||
<span><span class="co">#> 1 S</span></span>
|
||||
<span><span class="co">#> 2 R</span></span>
|
||||
<span><span class="co">#> 3 S</span></span>
|
||||
<span><span class="co">#> 4 S</span></span>
|
||||
<span><span class="co">#> 4 I</span></span>
|
||||
<span><span class="co">#> 5 R</span></span>
|
||||
<span><span class="co">#> 6 S</span></span></code></pre></div>
|
||||
<span><span class="co">#> 6 I</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
@ -438,40 +438,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3251</td>
|
||||
<td align="right">65.02%</td>
|
||||
<td align="right">3251</td>
|
||||
<td align="right">65.02%</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">971</td>
|
||||
<td align="right">19.42%</td>
|
||||
<td align="right">4222</td>
|
||||
<td align="right">84.44%</td>
|
||||
<td align="right">1016</td>
|
||||
<td align="right">20.32%</td>
|
||||
<td align="right">4230</td>
|
||||
<td align="right">84.60%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">468</td>
|
||||
<td align="right">9.36%</td>
|
||||
<td align="right">4690</td>
|
||||
<td align="right">93.80%</td>
|
||||
<td align="right">424</td>
|
||||
<td align="right">8.48%</td>
|
||||
<td align="right">4654</td>
|
||||
<td align="right">93.08%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">226</td>
|
||||
<td align="right">4.52%</td>
|
||||
<td align="right">4916</td>
|
||||
<td align="right">98.32%</td>
|
||||
<td align="right">247</td>
|
||||
<td align="right">4.94%</td>
|
||||
<td align="right">4901</td>
|
||||
<td align="right">98.02%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">84</td>
|
||||
<td align="right">1.68%</td>
|
||||
<td align="right">99</td>
|
||||
<td align="right">1.98%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -290,7 +290,7 @@ function:</p>
|
||||
<span><span class="co">#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
|
||||
<span><span class="co">#> Importance of components:</span></span>
|
||||
<span><span class="co">#> PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
|
||||
<span><span class="co">#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
|
||||
<span><span class="co">#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
|
||||
<span><span class="co">#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
|
||||
<span><span class="co">#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
|
||||
<pre><code><span><span class="co">#> Groups (n=4, named as 'order'):</span></span>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -178,7 +178,7 @@
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs
|
||||
Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">20 March 2023</h4>
|
||||
<h4 data-toc-skip class="date">14 April 2023</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>SPSS.Rmd</code></div>
|
||||
@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">484 734
|
||||
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">486 808
|
||||
R-related questions</a> have already been asked on this platform (that
|
||||
covers questions and answers for any programming language). In my own
|
||||
experience, most questions are answered within a couple of
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -322,7 +322,7 @@ Longest: 40</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">8</td>
|
||||
<td align="left">Staphylococcus capitis</td>
|
||||
<td align="left">Staphylococcus capitis urealyticus</td>
|
||||
<td align="right">8</td>
|
||||
<td align="right">1.6%</td>
|
||||
<td align="right">434</td>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -176,7 +176,7 @@
|
||||
<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">20 March 2023</h4>
|
||||
<h4 data-toc-skip class="date">14 April 2023</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="d-none name"><code>datasets.Rmd</code></div>
|
||||
@ -197,7 +197,7 @@ of the data sets look like.</p>
|
||||
<h2 id="microorganisms-full-microbial-taxonomy">
|
||||
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
|
||||
</h2>
|
||||
<p>A data set with 52 142 rows and 22 columns, containing the following
|
||||
<p>A data set with 52 149 rows and 22 columns, containing the following
|
||||
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
|
||||
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
|
||||
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
|
||||
@ -206,7 +206,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
|
||||
<em>gbif_renamed_to</em>, <em>prevalence</em>, and <em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 26 February 2023 20:26:58 UTC. Find more info
|
||||
<p>It was last updated on 14 April 2023 09:12:26 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@ -283,7 +283,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Bacteria</td>
|
||||
<td align="center">36 476</td>
|
||||
<td align="center">36 483</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Fungi</td>
|
||||
|
||||
@ -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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
@ -251,7 +251,7 @@ resistance and the standard error below and above the estimation:</p>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 61 0.016<span style="text-decoration: underline;">4</span> 0.106 </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 53 0.056<span style="text-decoration: underline;">6</span> 0.116 </span></span>
|
||||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>011 0.183 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 93 0.183 0.127 </span></span>
|
||||
<span><span class="co">#> <span style="color: #949494;"># … with 22 more rows</span></span></span></code></pre></div>
|
||||
<span><span class="co">#> <span style="color: #949494;"># ℹ 22 more rows</span></span></span></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be
|
||||
extended by other packages to depend the output based on the type of
|
||||
input. We extended its function to cope with resistance predictions:</p>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
|
||||
|
||||
Reference in New Issue
Block a user