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Built site for AMR: 1.8.2.9024@74bcc41

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2022-10-20 17:46:07 +00:00
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reference/age.html
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@ -190,16 +190,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1968-06-09 54 54.36438 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1986-02-19 36 36.66575 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1936-04-08 86 86.53425 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1965-09-02 57 57.13151 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1945-04-27 77 77.48219 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-02-16 34 34.67397 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1953-02-11 69 69.68767 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1976-01-29 46 46.72329 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1944-01-06 78 78.78630 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1997-02-24 25 25.65205 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1955-02-11 67 67.68767 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1965-04-20 57 57.50137 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1995-01-28 27 27.72603 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-03-04 43 43.63014 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1975-09-03 47 47.12877 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1990-02-11 32 32.68767 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1994-05-12 28 28.44110 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1980-04-21 42 42.49863 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1945-01-06 77 77.78630 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1938-06-07 84 84.36986 61</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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reference/as.rsi.html
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@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
<span class="r-out co"><span class="r-pr">#&gt;</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-20 <span style="color: #949494;">14:11:52</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-20 <span style="color: #949494;">14:11:52</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-20 <span style="color: #949494;">14:11:53</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-20 <span style="color: #949494;">14:11:53</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-20 <span style="color: #949494;">14:11:53</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-20 <span style="color: #949494;">14:11:53</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-20 <span style="color: #949494;">14:11:54</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-20 <span style="color: #949494;">14:11:54</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-20 <span style="color: #949494;">14:11:54</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-20 <span style="color: #949494;">14:11:54</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-20 <span style="color: #949494;">17:43:03</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-20 <span style="color: #949494;">17:43:04</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-20 <span style="color: #949494;">17:43:05</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>

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reference/get_episode.html
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@ -177,42 +177,42 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</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="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 38 54 24 6 7 33 20 44 53 63 25 55 56 49 61 62 9 8 45 9 36 17 37 2 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 35 20 13 11 23 63 59 61 43 59 41 25 22 12 46 18 62 57 17 27 8 36 29 24 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 58 35 61 48 12 18 3 31 20 41 56 9 56 51 64 16 1 36 40 50 53 19 25 36 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 20 9 18 36 62 29 51 45 12 10 23 40 3 38 5 15 7 17 21 3 63 38 40 7 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 63 7 17 15 51 17 62 2 61 12 52 32 46 32 27 4 13 61 19 37 41 38 51 22 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 41 14 12 29 64 58 52 57 46 57 33 56 16 34 26 5 34 17 42 63 61 22 58 20 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 25 38 25 17 12 22 56 28 13 34 3 47 25 63 16 1 5 1 22 39 31 14 31 51 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 1 61 46 6 27 19 1 56 40 30 20 10 57 60 18 24 60 30 22 47 23 62 26 62 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 51 1 30 33 57 38 63 41 55 28 20 27 45 11 12 55 39 3 21 59 25 21 9 2 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 49 24 11 32 51 28 21 38 57 36 11 54 24 36 60 6 50 31 60 47 43 20 54 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 40 35 12 62 31 42 41 37 9 20 1 2 34 48 46 45 51 36 59 45 62 28 54 26 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 44 49 28 19 17 10 62 40 6 8 38 51 32 5 37 46 7 61 51 38 27 52 33 58 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 38 1 41 7 48 43 9 17 14 31 16 60 19 54 54 28 24 31 54 35 54 3 6 15 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 48 34 34 60 29 41 12 19 57 54 50 45 17 56 62 10 28 13 28 4 33 53 54 47 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 56 31 9 49 40 61 33 11 50 27 23 24 44 15 4 8 30 48 28 61 62 3 40 60 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 21 26 25 4 13 10 3 8 54 63 48 64 64 44 42 47 58 53 14 8 52 22 13 17 23</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-16 241328 78 M Outpatie… B_STPHY_CONS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-11 974319 78 M Outpatie… B_STPHY_EPDR S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-18 E55128 57 F ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-09-23 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@ -248,16 +248,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 687590 2011-10-29 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C54153 2015-08-09 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 1710B8 2008-01-22 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 914520 2003-07-11 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 999565 2003-10-09 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 953526 2010-04-23 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311 2006-11-10 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 298662 2013-03-12 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2C8499 2015-05-22 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> F67215 2017-08-15 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> D53062 2014-07-28 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 495616 2002-01-17 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 534816 2008-10-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D30712 2009-04-10 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 2016-08-07 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 080086 2010-08-08 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 470001 2017-10-04 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F15984 2011-04-01 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D41749 2015-12-15 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 945BD5 2008-05-06 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -269,19 +269,19 @@
<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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [189]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2011-10-29 687590 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2015-08-09 C54153 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-01-22 1710B8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-07-11 914520 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2003-10-09 999565 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2010-04-23 953526 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2006-11-10 418311 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2013-03-12 298662 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2015-05-22 2C8499 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2017-08-15 F67215 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [185]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2014-07-28 D53062 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-01-17 495616 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-10-28 534816 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2009-04-10 D30712 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2016-08-07 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-08-08 080086 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2017-10-04 470001 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Outpatient 2011-04-01 F15984 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2015-12-15 D41749 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-05-06 945BD5 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -296,9 +296,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 119 14 48 72</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 59 14 37 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 8 9 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 116 14 53 71</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 52 11 32 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 17 10 16 17</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</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="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -328,19 +328,19 @@
<span class="r-in"><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="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [193]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 687590 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C54153 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 1710B8 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 914520 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 999565 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 953526 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311 B_STPHY_CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 298662 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2C8499 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> F67215 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> D53062 B_HMPHL_INFL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 495616 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 534816 F_CANDD_ALBC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D30712 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 080086 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 470001 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F15984 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> D41749 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 945BD5 B_ENTRBC_CLOC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

4
reference/kurtosis.html
View File

@ -167,9 +167,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.100538</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.993252</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02950212</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03411978</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

77
reference/mean_amr_distance.html
View File

@ -195,11 +195,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 128 2 4 256 &lt;=0.001 &lt;=0.001 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 128 0.01 0.001 128 0.025 16 4 64 0.25 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.38501534 1.16834939 0.22834853 0.38501534 1.32501620 -1.48962591</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.48962591 0.38501534 0.07168172 -0.96919003</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.8219432 0.9802175 -1.1792542 -1.7050300 0.9802175 -0.9700270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5053947 0.1888461 0.8219432 -0.4442511</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -209,38 +208,38 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</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="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.25 1 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 &gt;=2 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.025 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 &gt;=2 4 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &gt;=16 0.025 4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=16 0.125 0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=2 &gt;=2 0.25 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 0.025 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.0625 0.25 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.125 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 1 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 1 8 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=2 1 2 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=2 &lt;=0.025 1 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.0625 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 2 8 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 16 &gt;=4</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2679478 -0.2300449 -0.6609425 0.2703257 0.6591997 0.3959389</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.1096818 -0.4920944 -0.4283259 0.3276773</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.07272768 0.02436854 0.07054523 0.81400616 -0.47677206 -1.27310062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.30764224 0.49475116 -0.33800496 1.06457646</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.025 0.5 4 -0.6609425</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 0.025 2 2 -0.4920944</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=16 0.0625 0.25 &lt;=1 -0.4283259</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &lt;=2 &gt;=2 1 &lt;=1 -0.2300449</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &lt;=2 &gt;=2 0.25 8 -0.1096818</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.25 1 &gt;=16 0.2679478</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 &gt;=2 4 &lt;=1 0.2703257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 8 0.3276773</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=16 0.125 0.5 &gt;=16 0.3959389</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &gt;=16 0.025 4 &gt;=16 0.6591997</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &lt;=2 &lt;=0.025 1 &lt;=0.5 -1.27310062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E &lt;=2 1 2 &lt;=0.5 -0.47677206</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 0.5 2 -0.33800496</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 0.0625 1 2 -0.30764224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.125 2 &gt;=4 -0.07272768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5 0.02436854</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 1 2 &gt;=4 0.07054523</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &lt;=2 2 8 &gt;=4 0.49475116</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 1 8 &gt;=4 0.81400616</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 16 &gt;=4 1.06457646</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -252,17 +251,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &lt;=2 0.025 0.5 4 -0.6609425 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H &lt;=2 0.025 2 2 -0.4920944 0.1688482</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I &gt;=16 0.0625 0.25 &lt;=1 -0.4283259 0.2326166</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B &lt;=2 &gt;=2 1 &lt;=1 -0.2300449 0.4308977</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 G &lt;=2 &gt;=2 0.25 8 -0.1096818 0.5512607</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 4 0.25 1 &gt;=16 0.2679478 0.9288903</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D 4 &gt;=2 4 &lt;=1 0.2703257 0.9312683</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J 8 0.025 4 8 0.3276773 0.9886199</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F &gt;=16 0.125 0.5 &gt;=16 0.3959389 1.0568815</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E &gt;=16 0.025 4 &gt;=16 0.6591997 1.3201423</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &lt;=2 1 2 &gt;=4 0.07054523 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 0.25 8 &lt;=0.5 0.02436854 0.04617669</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A 4 0.125 2 &gt;=4 -0.07272768 0.14327291</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 8 0.0625 1 2 -0.30764224 0.37818747</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 8 0.125 0.5 2 -0.33800496 0.40855018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H &lt;=2 2 8 &gt;=4 0.49475116 0.42420593</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E &lt;=2 1 2 &lt;=0.5 -0.47677206 0.54731729</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 8 1 8 &gt;=4 0.81400616 0.74346093</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J &gt;=16 0.5 16 &gt;=4 1.06457646 0.99403123</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F &lt;=2 &lt;=0.025 1 &lt;=0.5 -1.27310062 1.34364585</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</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">%&gt;%</a></span></span></span>

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33
reference/random.html
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@ -178,43 +178,42 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.001 16 &gt;=256 0.002 16 64 2 16 0.125 0.001 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.001 0.01 64 0.001 0.002 128 0.5 32 1 0.001 2 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.01 64 0.5 &lt;=0.001 64 4 8 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 16 0.25 0.005 0.125 0.005 &lt;=0.001 4 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 0.01 0.125 4 64 0.002 &gt;=128 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 40 42 6 12 20 44 35 47 47 49 11 41 10 9 7 35 32 48 13 28 15 37 35 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 48 50 43 37 6 35 42 37 19 33 47 50 45 48 44 47 26 15 23 42 15 38 30 38</span>
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I S I S S I I I I R R I I R R R S S I R R I R R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S I I S S I S R R S I S I I R R I S S R S I I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 1 32 64 &lt;=0.001 2 0.025 8 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 32 0.002 0.005 2 0.025 0.005 0.025 128 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 32 8 128 0.005 1 0.01 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 0.5 1 0.005 2 0.01 16 0.25 128 0.002 8 0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 32 16 16 0.001 4 0.005 16 0.125 0.25 8 0.5 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 32 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.5 &gt;=16 1 4 &gt;=16 &gt;=16 2 &gt;=16 8 1 &lt;=0.5 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=16 4 2 2 8 2 2 4 1 8 &gt;=16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 &lt;=1 2 16 &lt;=1 &gt;=64 &lt;=1 32 4 &lt;=1 2 16 2 2 &gt;=64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &gt;=64 2 8 32 &gt;=64 8 8 4 &lt;=1 16 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.025 &lt;=0.025 0.5 0.125 &lt;=0.025 &lt;=0.025 16 0.5 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 8 1 2 16 16 &lt;=0.025 16 0.5 &lt;=0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.25 4 2 0.125 1 1 &lt;=0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 8 2 &lt;=0.125 0.5 &lt;=0.125 0.5 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.5 8 &lt;=0.125 2 1 2 0.25 1 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 2 1 0.25 0.5 8 0.25 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 34 18 36 49 44 12 50 42 50 50 28 17 42 40 16 44 24 44 48 10 15 49 49 16 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 49 37 14 42 20 48 28 49 28 47 21 35 34 35 36 49 31 18 39 25 50 23 32 26</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 14 16 16 17 16 16 16 17 13 14 11 15 11 17 12 13 13 14 14 17 16 11 14 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 11 14 12 16 13 15 11 12 14 14 13 13 12 16 14 11 12 11 11 13 15 17 13 16</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 17 15 19 25 23 27 23 15 22 23 17 16 27 22 21 20 19 17 20 25 15 26 24 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 23 20 17 18 15 20 26 22 26 16 23 23 27 20 18 18 17 25 27 27 15 19 19 19</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/skewness.html
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@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0329977</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0958419</span>
</code></pre></div>
</div>
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