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@ -62,7 +62,7 @@ Principal component analysis for AMR
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@ -10,7 +10,7 @@
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reference/age.html
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@ -10,7 +10,7 @@
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@ -195,16 +195,16 @@
<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 1996-03-04 26 26.76712 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1942-04-19 80 80.64110 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1931-08-02 91 91.35342 68</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1976-12-11 45 45.99452 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1978-12-19 43 43.97260 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1958-05-13 64 64.57534 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1951-12-07 71 71.00548 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1962-12-05 60 60.01096 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1951-09-05 71 71.26027 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1967-10-18 55 55.14247 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1976-08-21 46 46.30137 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-03-07 69 69.75890 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1940-02-25 82 82.78630 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1972-05-17 50 50.56438 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1944-12-05 78 78.01096 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1991-05-13 31 31.57534 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1960-07-24 62 62.37808 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1982-06-27 40 40.45205 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1993-07-18 29 29.39452 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1951-10-24 71 71.12603 48</span>
</code></pre></div>
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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reference/as.mo.html
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@ -10,7 +10,7 @@
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reference/as.rsi.html
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@ -10,7 +10,7 @@
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@ -506,16 +506,16 @@ 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 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</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> 2022-12-09 <span style="color: #949494;">12:41:48</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> 2022-12-09 <span style="color: #949494;">12:41:49</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-09 <span style="color: #949494;">12:41:49</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-09 <span style="color: #949494;">12:41:50</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-09 <span style="color: #949494;">12:41:50</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-09 <span style="color: #949494;">12:41:50</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> 2022-12-09 <span style="color: #949494;">12:41:51</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> 2022-12-09 <span style="color: #949494;">12:41:51</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> 2022-12-09 <span style="color: #949494;">12:41:51</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> 2022-12-09 <span style="color: #949494;">12:41:51</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> 2022-12-09 <span style="color: #949494;">14:14:44</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> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-09 <span style="color: #949494;">14:14:45</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-09 <span style="color: #949494;">14:14:46</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> 2022-12-09 <span style="color: #949494;">14:14:46</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> 2022-12-09 <span style="color: #949494;">14:14:46</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> 2022-12-09 <span style="color: #949494;">14:14:46</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> 2022-12-09 <span style="color: #949494;">14:14:46</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, 5 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;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

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reference/atc_online.html
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@ -10,7 +10,7 @@
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">1.8.2.9058</small>
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2
reference/custom_eucast_rules.html
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@ -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="">1.8.2.9058</small>
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2
reference/dosage.html
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@ -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="">1.8.2.9058</small>
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2
reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">1.8.2.9058</small>
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2
reference/example_isolates.html
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@ -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="">1.8.2.9058</small>
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2
reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/first_isolate.html
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@ -12,7 +12,7 @@
<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="">1.8.2.9058</small>
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2
reference/g.test.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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144
reference/get_episode.html
View File

@ -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="">1.8.2.9058</small>
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@ -182,42 +182,42 @@
<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] 23 4 57 10 24 33 54 46 15 13 52 3 46 30 17 43 31 50 27 6 44 18 9 40 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 32 49 49 9 23 27 8 8 22 53 26 58 1 59 49 59 5 35 22 11 43 60 54 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 51 26 18 43 2 22 47 28 36 22 15 1 40 23 41 34 60 32 45 9 51 21 50 24 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 42 26 29 58 31 13 59 4 55 38 10 19 54 29 7 53 50 55 15 40 4 46 55 61 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 14 43 54 45 54 10 23 55 18 48 9 33 29 7 6 41 39 28 59 7 62 6 41 57 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 60 41 35 37 15 45 49 24 36 10 25 22 20 52 14 62 8 6 42 60 12 41 14 32 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 59 58 9 13 13 21 36 3 49 12 1 9 57 3 17 23 14 13 62 56 57 40 6 13 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 19 57 24 47 59 20 61 46 54 58 48 30 39 4 32 42 25 4 22 20 56 3 16 44 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 63 45 25 27 5 60 43 43 48 65 20 11 34 1 35 24 32 57 55 12 31 41 31 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 3 19 45 49 66 55 20 49 1 4 3 16 37 35 25 61 63 1 37 36 20 22 3 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 64 11 12 40 61 16 15 21 26 57 2 44 1 49 35 21 29 7 17 15 13 48 10 20 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 29 45 14 40 59 65 26 52 49 7 33 29 14 9 17 46 51 18 65 3 38 6 12 11 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 52 5 64 57 22 26 58 7 21 30 16 8 54 33 19 11 41 10 59 34 64 38 64 57 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 51 14 18 54 9 6 23 53 44 21 36 63 48 62 19 7 36 7 11 49 58 34 34 37 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 31 45 22 24 4 58 54 22 22 56 14 14 62 32 23 63 1 8 61 41 28 11 30 26 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 39 14 42 49 25 49 52 43 18 11 38 55 11 56 59 54 15 9 48 60 50 4 7 18 57</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] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE TRUE FALSE FALSE TRUE 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> 2002-08-31 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;">2</span> 2002-09-24 CF9318 29 M ICU B_CMPYL_JEJN NA NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-10-11 871360 78 M Clinical B_STPHY_EPDR R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-08-28 390178 57 M Clinical B_STRPT_SLVR S NA NA S </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> 2002-05-16 E52286 47 M Clinical B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-05-22 F35553 50 M ICU B_STPHY_EPDR R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-05-16 D25302 65 F ICU B_STRPT_ANGN S NA NA S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-07 710157 76 M Outpatie… B_STPHY_CONS 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>
@ -253,16 +253,16 @@
<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> 403631 2007-07-31 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304347 2002-11-04 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 964129 2016-06-21 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 189363 2004-03-17 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 80C025 2007-11-13 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 284FFF 2010-03-31 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A76045 2015-10-06 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 959835 2013-11-16 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 277241 2005-09-01 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 696587 2004-11-16 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 399817 2004-04-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C95287 2017-03-14 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A95779 2012-05-18 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 636118 2007-06-17 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 921720 2007-11-02 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 600057 2002-11-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D10538 2016-08-13 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 146120 2011-09-23 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 685406 2011-09-27 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C01360 2013-07-27 B 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>
@ -274,19 +274,19 @@
<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 [179]</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 2007-07-31 403631 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-11-04 304347 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2016-06-21 964129 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2004-03-17 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-11-13 80C025 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-03-31 284FFF 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2015-10-06 A76045 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2013-11-16 959835 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2005-09-01 277241 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2004-11-16 696587 1 FALSE </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 2004-04-15 399817 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-03-14 C95287 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2012-05-18 A95779 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-06-17 636118 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-11-02 921720 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2002-11-28 600057 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2016-08-13 D10538 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-09-23 146120 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2011-09-27 685406 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2013-07-27 C01360 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>
@ -301,9 +301,9 @@
<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 112 14 57 81</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 53 13 37 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 14 8 11 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 104 14 53 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 65 12 40 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 16 9 16 16</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>
@ -322,7 +322,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</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"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@ -333,19 +333,19 @@
<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 [186]</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> 403631 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304347 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 964129 B_SERRT_MRCS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 189363 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 80C025 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 284FFF B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> A76045 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 959835 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 277241 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 696587 B_ESCHR_COLI ICU FALSE </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> 399817 B_CTRBC_FRND Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C95287 B_STPHY_HMNS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A95779 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 636118 B_MRGNL_MRGN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 921720 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 600057 B_STPHY_AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D10538 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 146120 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 685406 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C01360 B_STPHY_CONS 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>

2
reference/ggplot_pca.html
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@ -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="">1.8.2.9058</small>
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2
reference/ggplot_rsi.html
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@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
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2
reference/guess_ab_col.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
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2
reference/index.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/intrinsic_resistant.html
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@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/italicise_taxonomy.html
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@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
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2
reference/join.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
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2
reference/key_antimicrobials.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

6
reference/kurtosis.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">
@ -172,9 +172,9 @@
<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] 2.991918</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.143253</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] -0.0630367</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.07895301</span>
</code></pre></div>
</div>
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2
reference/like.html
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@ -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="">1.8.2.9058</small>
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2
reference/mdro.html
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@ -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="">1.8.2.9058</small>
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79
reference/mean_amr_distance.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">
@ -200,11 +200,10 @@
<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] &gt;=128 2 32 &lt;=0.002 64 &lt;=0.002 0.005 8 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 &gt;=2 0.005 0.01 &gt;=2 1 0.5 0.001 0.001 0.002</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] 1.0898120 0.1928148 0.7908130 -1.2970653 0.9403125 -1.2970653</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.0994377 0.4918139 -0.7523105 0.9403125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.3309983 1.2029031 -0.6812519 -0.4632756 1.2029031 0.9849269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7669507 -1.1873769 -1.1873769 -0.9694007</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>
@ -214,38 +213,38 @@
<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 16 &lt;=0.0625 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 &lt;=0.0625 0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.25 0.25 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=32 0.5 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.25 0.25 4</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 32 0.25 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 &gt;=1 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=1 &lt;=0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.5 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 1 0.25 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.5 &gt;=8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.125 1 2</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] -0.15596821 -0.35223027 -0.06296188 -0.77906287 -0.19333099 1.00776983</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.64235988 0.64363737 1.00124386 -0.46673697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12196526 0.40284317 -0.47762168 -0.30700434 -0.06650357 0.79277984</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.73763891 0.32070406 0.19485787 -0.24438169</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> 4 D 8 &lt;=0.0625 0.5 &lt;=0.5 -0.77906287</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 0.5 1 -0.64235988</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 4 0.25 0.25 4 -0.46673697</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.5 0.5 1 -0.35223027</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 0.25 0.25 &gt;=16 -0.19333099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 16 &lt;=0.0625 0.5 4 -0.15596821</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 0.5 &lt;=0.5 -0.06296188</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H &gt;=32 0.5 1 2 0.64363737</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16 1.00124386</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.5 4 4 1.00776983</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> 7 G 1 0.25 2 &lt;=1 -0.73763891</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 2 &gt;=1 &lt;=0.5 &lt;=1 -0.47762168</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 8 0.5 1 &lt;=1 -0.30700434</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 32 &lt;=0.125 1 2 -0.24438169</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1 -0.06650357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.25 &lt;=0.5 4 0.12196526</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.5 &gt;=8 &lt;=1 0.19485787</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.32070406</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 &gt;=1 1 4 0.40284317</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 &gt;=8 &lt;=1 0.79277984</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>
@ -257,17 +256,17 @@
<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 16 0.5 0.5 &lt;=0.5 -0.06296188 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 16 &lt;=0.0625 0.5 4 -0.15596821 0.09300632</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E 4 0.25 0.25 &gt;=16 -0.19333099 0.13036910</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B 4 0.5 0.5 1 -0.35223027 0.28926839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J 4 0.25 0.25 4 -0.46673697 0.40377508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 8 &lt;=0.0625 0.5 1 -0.64235988 0.57939799</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 H &gt;=32 0.5 1 2 0.64363737 0.70659925</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 8 &lt;=0.0625 0.5 &lt;=0.5 -0.77906287 0.71610098</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=32 1 0.5 &gt;=16 1.00124386 1.06420574</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 16 0.5 4 4 1.00776983 1.07073172</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 2 &gt;=1 &lt;=0.5 &lt;=1 -0.47762168 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 D 8 0.5 1 &lt;=1 -0.30700434 0.1706173</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 32 &lt;=0.125 1 2 -0.24438169 0.2332400</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 1 0.25 2 &lt;=1 -0.73763891 0.2600172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 1 &lt;=1 -0.06650357 0.4111181</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 32 0.25 &lt;=0.5 4 0.12196526 0.5995869</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I 8 0.5 &gt;=8 &lt;=1 0.19485787 0.6724795</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 2 &gt;=1 4 2 0.32070406 0.7983257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B 4 &gt;=1 1 4 0.40284317 0.8804648</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F &gt;=64 &gt;=1 &gt;=8 &lt;=1 0.79277984 1.2704015</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>

2
reference/microorganisms.codes.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/microorganisms.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/mo_matching_score.html
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@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/mo_property.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/mo_source.html
View File

@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/pca.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

BIN
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2
reference/plot.html
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@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

2
reference/proportion.html
View File

@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">

36
reference/random.html
View File

@ -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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</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">
@ -183,42 +183,44 @@
<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] 8 0.25 0.01 8 128 0.025 0.5 &lt;=0.002 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 16 0.005 0.005 0.025 0.025 0.25 0.025 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 256 256 2 256 0.005 0.025 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 64 0.0625 0.025 0.25 0.025 0.01 0.005 128 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 64 32 0.125 0.002 0.005 64 0.0625 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 128 0.0625 &lt;=0.001 0.002 0.0625 0.25 </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] 30 16 47 35 37 49 26 34 44 48 27 44 26 41 49 23 7 50 19 34 38 25 21 43 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 47 11 44 36 21 24 31 13 40 21 42 33 36 18 41 40 15 19 26 48 8 11 37 46</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] R S S S S I S S R R R I S S S S S S S S R I R I S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S R R I S R I R I R R R I R I R S R R R I S S</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] 1 128 0.001 0.01 128 0.01 0.001 0.01 4 128 0.001 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.002 4 16 32 1 0.25 1 2 64 16 64 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 0.5 0.01 16 8 0.0625 &lt;=0.001 0.0625 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4 8 &lt;=0.001 0.002 4 &lt;=0.001 0.0625 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.01 0.01 &lt;=0.001 0.002 0.025 2 0.5 </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;=1 8 8 8 &lt;=1 2 4 8 &gt;=16 &gt;=16 2 4 8 &gt;=16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 4 2 &gt;=16 4 &lt;=1 2 &gt;=16 8 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 16 16 8 16 1 8 8 4 16 4 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 &lt;=0.5 4 &lt;=0.5 16 1 2 8 16 &lt;=0.5 2 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </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] 1 2 &gt;=16 &gt;=16 4 2 0.5 0.5 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.5 &lt;=0.125 2 4 &gt;=16 4 8 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 1 &lt;=0.125 0.5 0.5 0.5 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 4 0.25 &lt;=0.0625 16 &lt;=0.0625 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.5 0.125 8 1 0.25 0.5 8 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] &lt;=0.0625 0.125 0.25 0.25 0.5 16 0.125 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.0625</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] 21 36 49 10 16 15 34 46 43 42 33 47 43 50 19 45 45 13 34 9 46 20 42 40 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 26 37 31 35 32 48 43 11 17 25 20 47 27 30 44 48 41 47 46 45 37 41 13 28</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] 16 11 16 13 11 12 11 14 13 11 14 11 12 15 12 12 13 13 17 17 16 13 16 11 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 16 14 12 17 11 14 11 12 11 16 12 16 11 16 12 14 17 12 13 14 15 17 15 11</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] 17 15 25 23 16 23 16 27 26 20 17 16 22 22 27 18 24 17 26 25 27 21 16 27 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 22 20 23 18 16 19 27 17 16 24 16 27 16 17 17 15 19 15 15 20 22 24 21 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9058</small>
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">1.8.2.9058</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9059</small>
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@ -171,7 +171,7 @@ 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] -0.01115228</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -9.41422e-05</span>
</code></pre></div>
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