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@ -7,7 +7,7 @@
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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="">2.1.1.9192</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9195</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -153,20 +153,20 @@
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<span class="r-in"><span><span class="va">df</span> <span class="op"><-</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">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 47 28 47 47 48 1 48 13 7 38 28 5 14 49 13 22 31 18 28 21 6 8 6 39 13</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 5 11 15 9 42 48 43 28 18 4 45 26 2 31 43 10 4 23 47 25 35 1 38 24 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [51] 19 4 16 5 16 1 44 39 41 25 4 11 30 1 17 30 3 48 8 39 6 38 5 20 37</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 36 44 31 48 40 42 43 44 33 12 4 10 34 11 8 12 32 10 33 29 46 34 27 22 23</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 12 40 46 27 46 46 47 1 47 13 7 37 27 5 14 48 13 22 30 18 27 21 6 8</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 6 38 13 5 11 15 9 41 47 42 27 18 4 44 26 2 30 42 10 4 23 46 25 34 1</span>
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<span class="r-out co"><span class="r-pr">#></span> [51] 37 24 15 19 4 16 5 16 1 43 38 40 25 4 11 29 1 17 29 3 47 8 38 6 37</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 5 20 36 35 43 30 47 39 41 42 43 32 12 4 10 33 11 8 12 31 10 32 28 45 33</span>
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<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [37] TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [13] TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE TRUE FALSE</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
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<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>
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@ -261,9 +261,9 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 57 14 38 48</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 56 13 36 47</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 31 12 25 28</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 6 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 7 5 7 7</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
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<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
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@ -293,18 +293,18 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
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<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> F5F794 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 146120 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 501607 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC ICU TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 402950 <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS ICU TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 560323 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 4FC193 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D80438 <span style="color: #949494;">B_</span>CRYNB<span style="color: #949494;">_</span>STRT Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F81262 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 619705 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>ANGN ICU TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 280834 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 969275 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Outpatient TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A87231 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> A84726 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>HMNS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F5F794 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 146120 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 501607 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC ICU TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 402950 <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS ICU TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 560323 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 4FC193 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D80438 <span style="color: #949494;">B_</span>CRYNB<span style="color: #949494;">_</span>STRT Clinical TRUE </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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