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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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@ -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 1934-10-18 88 88.03288 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1960-12-13 61 61.87945 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1953-09-24 69 69.09863 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1955-11-24 66 66.93151 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1974-02-22 48 48.68493 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1999-04-09 23 23.55890 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1966-12-21 55 55.85753 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1996-03-30 26 26.58630 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1932-08-29 90 90.16986 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1939-03-07 83 83.64932 60</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1949-12-04 72 72.90685 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1971-02-19 51 51.69589 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1941-10-11 81 81.05479 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1949-01-06 73 73.81644 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1963-06-21 59 59.36164 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-01-19 75 75.78082 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1983-11-29 38 38.92055 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1971-03-01 51 51.66849 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1969-05-29 53 53.42466 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1958-09-08 64 64.14521 41</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -496,16 +496,16 @@ 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> 2022-10-30 <span style="color: #949494;">20:10:34</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> 2022-10-30 <span style="color: #949494;">20:10:35</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> 2022-10-30 <span style="color: #949494;">20:10:35</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> 2022-10-30 <span style="color: #949494;">20:10:36</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> 2022-10-30 <span style="color: #949494;">20:10:36</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> 2022-10-30 <span style="color: #949494;">20:10:37</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> 2022-10-30 <span style="color: #949494;">20:10:37</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> 2022-10-30 <span style="color: #949494;">20:10:37</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> 2022-10-30 <span style="color: #949494;">20:10:38</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> 2022-10-30 <span style="color: #949494;">20:10:38</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> 2022-10-31 <span style="color: #949494;">10:24:50</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> 2022-10-31 <span style="color: #949494;">10:24:51</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> 2022-10-31 <span style="color: #949494;">10:24:51</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> 2022-10-31 <span style="color: #949494;">10:24:51</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> 2022-10-31 <span style="color: #949494;">10:24:52</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> 2022-10-31 <span style="color: #949494;">10:24:53</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> 2022-10-31 <span style="color: #949494;">10:24:53</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;"> 8</span> 2022-10-31 <span style="color: #949494;">10:24:53</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> 2022-10-31 <span style="color: #949494;">10:24:54</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> 2022-10-31 <span style="color: #949494;">10:24:54</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: #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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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/example_isolates.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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/example_isolates_unclean.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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/first_isolate.html
View File

@ -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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/g.test.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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">

140
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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">
@ -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] 62 16 19 48 19 56 61 35 35 19 63 41 12 60 21 53 7 28 10 50 8 2 24 11 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 36 5 56 41 12 9 50 27 61 26 53 1 54 1 52 34 27 23 61 56 66 14 33 64 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 37 1 5 60 1 11 32 25 3 44 56 29 30 27 7 64 11 28 56 6 17 31 38 51 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 61 10 51 38 43 48 55 43 54 24 37 11 7 3 64 48 6 64 10 55 14 7 39 9 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 31 16 15 58 21 42 62 8 59 48 56 28 1 47 22 64 57 13 49 57 58 9 35 19 64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 28 29 5 16 37 7 65 14 38 8 29 63 26 13 8 45 24 19 52 5 22 3 57 55 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 29 44 23 31 64 12 53 59 38 29 41 59 26 12 18 15 9 1 29 20 47 5 43 39 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 6 36 4 52 46 33 39 61 65 56 57 13 3 25 22 6 42 22 49 5 6 44 35 7 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 2 13 51 18 14 11 15 4 31 11 6 45 56 10 63 32 62 24 42 40 60 25 28 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 46 33 27 2 64 10 30 28 18 52 57 39 12 61 18 58 5 55 46 53 4 29 60 23 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 51 10 22 25 9 14 1 54 62 27 22 43 50 29 48 1 3 40 54 11 45 1 2 57 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 56 45 21 59 63 33 62 19 47 20 31 50 19 23 61 28 27 22 46 30 49 7 26 31 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 25 56 62 20 8 17 58 61 50 13 33 61 12 49 34 43 41 1 27 59 55 59 63 54 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 13 37 35 52 27 25 36 59 63 3 34 20 60 28 55 16 1 57 25 13 42 7 54 15 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 34 1 23 38 56 21 46 48 60 10 47 17 47 10 59 35 54 59 43 46 57 7 20 62 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 21 59 43 58 50 8 27 53 3 3 45 44 4 30 60 38 58 39 27 21 13 13 1 62 13</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 TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE 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 FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE 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 FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE TRUE FALSE FALSE FALSE 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> 2002-05-16 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;">2</span> 2002-05-22 F35553 50 M 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> 2002-06-06 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-19 402950 53 F Clinical B_STPHY_HMNS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-24 F35553 51 M 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> 2002-06-22 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;">4</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </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> 927431 2017-01-12 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 161740 2005-06-21 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 968584 2006-01-11 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 479516 2013-09-30 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F32657 2006-03-09 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 193126 2015-12-18 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E84349 2016-11-25 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 699321 2010-07-23 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 727637 2010-09-09 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> F32657 2006-03-09 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 318447 2004-05-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C70694 2002-05-15 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E48302 2004-11-29 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D60054 2014-10-16 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 5DF436 2006-01-04 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 4F6B71 2005-01-24 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 4B6270 2004-07-01 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A92398 2005-05-14 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F35553 2002-10-20 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A54805 2008-11-19 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>
@ -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 [188]</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 2017-01-12 927431 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2005-06-21 161740 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2006-01-11 968584 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2013-09-30 479516 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2006-03-09 F32657 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-12-18 193126 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2016-11-25 E84349 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-07-23 699321 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2010-09-09 727637 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2006-03-09 F32657 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [182]</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> Outpatient 2004-05-28 318447 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-05-15 C70694 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2004-11-29 E48302 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-10-16 D60054 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2006-01-04 5DF436 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2005-01-24 4F6B71 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-07-01 4B6270 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2005-05-14 A92398 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2002-10-20 F35553 3 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-11-19 A54805 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 116 14 55 75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57 12 33 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 15 7 12 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 116 15 56 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 56 13 33 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 5 8 8</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>
@ -317,7 +317,7 @@
<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>
@ -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 [192]</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> 927431 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 161740 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 968584 F_CANDD_ALBC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 479516 B_STPHY_HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F32657 B_CRYNB ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 193126 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E84349 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 699321 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 727637 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> F32657 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [189]</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> 318447 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C70694 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E48302 B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D60054 B_STRPT_SLVR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 5DF436 B_ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 4F6B71 B_STRPT_GRPB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 4B6270 B_PSDMN_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A92398 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F35553 B_STPHY_AURS ICU FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> A54805 B_STRPT_PNMN 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
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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/ggplot_rsi.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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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
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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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
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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">
@ -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] 3.057425</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.036334</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] 0.08177269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.03572271</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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/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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">

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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">
@ -195,10 +195,11 @@
<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] 0.125 128 0.5 0.001 0.002 32 0.01 0.0625 0.0625 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 128 &lt;=0.001 0.125 0.025 16 0.01 16 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.01 </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] 0.03977575 1.83205678 0.39823196 -1.20868855 -1.02946045 1.47360058</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.61330568 -0.13945235 -0.13945235 -0.61330568</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.8741078 1.1886741 -1.4797580 -0.3841574 -0.7493576 0.7168247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.9572746 0.7168247 1.0313910 -0.9572746</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>
@ -208,38 +209,38 @@
<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 &lt;=2 1 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.025 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.5 2 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 64 &gt;=2 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.25 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 0.125 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.25 &lt;=0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 64 &gt;=2 8 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 64 1 4 2</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 2 0.5 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 1 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 &gt;=2 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 1 0.25 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 1 &gt;=4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.25 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 2 1 &gt;=4 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=2 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 &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] -0.1805861 -0.3593922 -0.5470696 0.4524955 0.1519544 -0.3106839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1028200 -0.6317241 0.6651338 0.6570522</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.1488052 0.6945257 0.2690034 -1.1500416 0.3939183 -0.8331088</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5483034 -0.4739008 0.5987413 0.1013643</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> 8 H 16 0.25 &lt;=0.5 &lt;=1 -0.6317241</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &lt;=2 0.5 2 &lt;=1 -0.5470696</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 32 0.025 &lt;=0.5 4 -0.3593922</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 &lt;=0.5 4 -0.3106839</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=2 1 &lt;=0.5 4 -0.1805861</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 0.125 1 4 0.1028200</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.25 4 2 0.1519544</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 64 &gt;=2 1 2 0.4524955</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 64 1 4 2 0.6570522</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 64 &gt;=2 8 &lt;=1 0.6651338</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 1 0.25 2 1 -1.1500416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 1 0.25 2 2 -0.8331088</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.4739008</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 2 0.5 2 &gt;=4 -0.1488052</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 16 0.25 2 &gt;=4 0.1013643</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 8 &gt;=2 2 2 0.2690034</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 1 &gt;=4 &gt;=4 0.3939183</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 2 1 &gt;=4 &gt;=4 0.5483034</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 &gt;=2 &gt;=4 2 0.5987413</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 1 &gt;=4 2 0.6945257</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>
@ -251,17 +252,17 @@
<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 0.5 2 &lt;=1 -0.5470696 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 16 0.25 &lt;=0.5 &lt;=1 -0.6317241 0.0846545</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B 32 0.025 &lt;=0.5 4 -0.3593922 0.1876774</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 4 0.25 &lt;=0.5 4 -0.3106839 0.2363857</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A &lt;=2 1 &lt;=0.5 4 -0.1805861 0.3664836</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G 32 0.125 1 4 0.1028200 0.6498896</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 16 0.25 4 2 0.1519544 0.6990240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 64 &gt;=2 1 2 0.4524955 0.9995652</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 J 64 1 4 2 0.6570522 1.2041218</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I 64 &gt;=2 8 &lt;=1 0.6651338 1.2122034</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 8 &gt;=2 2 2 0.2690034 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E 1 1 &gt;=4 &gt;=4 0.3939183 0.1249149</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 16 0.25 2 &gt;=4 0.1013643 0.1676392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 G 2 1 &gt;=4 &gt;=4 0.5483034 0.2793000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 4 &gt;=2 &gt;=4 2 0.5987413 0.3297379</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A 2 0.5 2 &gt;=4 -0.1488052 0.4178086</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 16 1 &gt;=4 2 0.6945257 0.4255223</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.4739008 0.7429042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 1 0.25 2 2 -0.8331088 1.1021122</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D 1 0.25 2 1 -1.1500416 1.4190451</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
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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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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
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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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">

35
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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,43 +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] 0.01 256 2 2 256 1 0.001 64 0.01 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 128 16 64 0.0625 16 128 0.0625 256 2 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 128 0.01 8 64 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.025 0.0625 8 4 &gt;=64 2 0.025 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.0625 4 &lt;=0.002 32 0.025 0.01 0.125 8 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625 0.01 &lt;=0.002 0.005 1 0.125 &lt;=0.002</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] 22 38 41 24 23 27 40 16 21 48 10 47 30 44 20 25 29 30 33 19 12 45 19 24 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 6 18 6 12 41 34 46 48 22 6 8 35 45 35 39 23 11 12 42 26 35 39 40 16</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] S S I I S R S S S S S S R I R I I I R I R I R S I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S R S S S S I R R R S R S I R S R I S R R R S 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] 8 2 0.125 32 4 &lt;=0.001 0.0625 0.25 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 32 8 &lt;=0.001 &lt;=0.001 4 0.025 0.005 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625 0.002 0.005 0.025 64 0.025 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 4 32 0.125 128 0.25 0.025 &lt;=0.001 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.005 &lt;=0.001 2 4 0.005 1 0.005 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 8 64 128 4 1 128 4 </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] 16 1 4 16 32 8 16 &lt;=0.5 32 4 64 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 64 &lt;=0.5 1 8 1 1 &lt;=0.5 1 16 &lt;=0.5 8 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 2 4 1 32 4 0.5 2 16 0.25 &gt;=64 1 0.5 2 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 1 &gt;=64 32 &gt;=64 16 1 0.5 8 8 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">"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] 0.5 0.5 1 1 8 16 4 0.125 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 1 1 8 &lt;=0.025 16 4 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1 4 2 0.0625 0.125 &lt;=0.025 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.025 0.125 0.5 1 8 0.25 0.025 4 0.25 0.125 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 0.5 0.125 2 8 4 0.125 0.5 8 0.25 0.025 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </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] 17 22 48 47 18 37 40 13 34 50 33 31 14 30 24 34 13 21 43 31 36 33 45 46 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40 44 38 42 13 50 38 49 45 46 32 45 17 50 31 27 43 40 19 47 45 22 19 26 41</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] 12 17 11 11 15 14 14 13 14 11 13 11 16 15 12 14 17 11 17 14 13 17 16 13 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 16 13 13 14 12 12 13 12 12 11 14 11 13 11 14 15 17 11 14 12 13 13 14 12</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 16 18 18 22 16 21 25 15 22 25 26 26 26 19 22 25 19 24 27 23 20 17 23 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 23 17 20 23 15 16 15 15 21 22 17 22 23 22 23 17 15 16 24 18 24 26 23 18</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

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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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
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<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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</small>
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reference/skewness.html
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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="">1.8.2.9039</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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">
@ -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] -0.03383025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0247852</span>
</code></pre></div>
</div>
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<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="">1.8.2.9039</small>
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