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<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
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@ -80,7 +80,7 @@
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
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@ -93,12 +93,65 @@
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Home
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<a href="../articles/AMR.html">
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Get Started
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How to
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<a href="../articles/AMR.html">
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Conduct AMR analysis
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<a href="../articles/Predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Create frequency tables
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Use the G-test
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@ -121,17 +174,17 @@
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Changelog
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@ -199,49 +252,51 @@
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</ul></li>
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<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='age.html'>age</a></code> to determine ages based on one or more reference dates</p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='no'>ages</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='no'>ages</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
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<span class='co'># split into 0-49 and 50+</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)</div><div class='output co'>#> [1] 0-49 0-49 0-49 50+ 0-49 50+ 50+ 0-49 0-49
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#> Levels: 0-49 < 50+</div><div class='input'>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>50</span>)
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<span class='co'># split into 0-19, 20-49 and 50+</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))</div><div class='output co'>#> [1] 0-19 0-19 0-19 50+ 20-49 50+ 50+ 20-49 20-49
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#> Levels: 0-19 < 20-49 < 50+</div><div class='input'>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
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<span class='co'># split into groups of ten years</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)</div><div class='output co'>#> [1] 0-9 0-9 10-19 50-59 30-39 70-79 100+ 40-49 20-29
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#> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+</div><div class='input'><span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)</div><div class='output co'>#> [1] 0-9 0-9 10-19 50-59 30-39 70-79 100+ 40-49 20-29
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#> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+</div><div class='input'>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>10</span> * <span class='fl'>10</span>)
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"tens"</span>)
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<span class='co'># split into groups of five years</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)</div><div class='output co'>#> [1] 0-4 5-9 15-19 50-54 30-34 75-79 100+ 40-44 20-24
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#> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+</div><div class='input'><span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)</div><div class='output co'>#> [1] 0-4 5-9 15-19 50-54 30-34 75-79 100+ 40-44 20-24
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#> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+</div><div class='input'>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fl'>1</span>:<span class='fl'>20</span> * <span class='fl'>5</span>)
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='kw'>split_at</span> <span class='kw'>=</span> <span class='st'>"fives"</span>)
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<span class='co'># split specifically for children</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)</div><div class='output co'>#> [1] 2-3 6-12 13-17 18+ 18+ 18+ 18+ 18+ 18+
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#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+</div><div class='input'><span class='co'># same:</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))</div><div class='output co'>#> [1] 2-3 6-12 13-16 17+ 17+ 17+ 17+ 17+ 17+
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#> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-16 < 17+</div><div class='input'>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='st'>"children"</span>)
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<span class='co'># same:</span>
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<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
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<span class='co'># resistance of ciprofloxacine per age group</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)</div><div class='output co'>#> <span class='message'></span>
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#> <span class='message'>Attaching package: ‘dplyr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:testthat’:</span>
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#> <span class='message'></span>
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#> <span class='message'> matches</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:stats’:</span>
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#> <span class='message'></span>
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#> <span class='message'> filter, lag</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:base’:</span>
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#> <span class='message'></span>
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#> <span class='message'> intersect, setdiff, setequal, union</span></div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/mutate'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/filter'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>age_group</span>,
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<span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>date</span><span style='color: #0000BB;'>` as input for `col_date`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>patient_id</span><span style='color: #0000BB;'>` as input for `col_patient_id`.</span><span></span></div><div class='output co'>#> <span class='message'>=> Found </span><span style='font-weight: bold;'>1,317 first isolates</span><span> (65.9% of total)</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 3 rows containing missing values (geom_bar).</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 3 rows containing missing values (geom_text).</span></div><div class='img'><img src='age_groups-1.png' alt='' width='700' height='433' /></div></span></pre>
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<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
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<span class='co'># }</span></pre>
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</div>
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<h2>Contents</h2>
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<li><a href="#details">Details</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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