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Built site for AMR: 1.8.1.9049@63fe160
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github-actions
@ -10,7 +10,7 @@
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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="">1.8.1.9047</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</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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@ -177,39 +177,41 @@
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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">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>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 53 18 52 33 48 33 11 63 36 51 38 25 17 19 32 18 28 9 65 43 38 17 51 1 19</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 12 35 40 22 10 37 48 49 53 41 19 30 7 54 19 28 25 20 25 14 57 1 47 49 29</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 34 66 27 18 10 28 54 51 52 6 34 26 4 35 64 29 32 25 14 35 28 22 27 33 55</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [76] 44 45 12 46 13 59 53 46 60 13 41 53 42 10 30 64 18 25 59 3 65 32 44 15 16</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [101] 58 2 44 23 21 42 26 41 14 17 16 64 25 50 8 11 63 37 30 28 27 52 53 4 25</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [126] 35 28 45 9 7 61 50 1 53 19 1 58 11 39 21 43 6 24 40 2 63 6 27 16 63</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [151] 41 36 20 23 57 5 64 47 29 58 2 30 57 8 25 11 15 13 14 52 7 31 1 27 62</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [176] 65 60 25 29 7 1 56 55 49 65 28 64 33 26 46 1 18 22 64 14 63 10 66 59 13</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 47 61 41 30 22 55 11 62 22 52 58 11 11 17 15 28 11 13 37 59 31 18 8 48 41</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [26] 45 3 64 1 53 8 64 55 62 41 23 58 64 51 18 16 8 64 40 47 50 20 9 15 31</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 24 58 8 37 7 21 67 30 17 14 1 43 41 9 17 45 44 13 21 31 29 39 2 66 36</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [76] 12 61 52 30 67 58 65 63 30 56 26 60 66 40 60 43 51 35 65 64 7 64 25 54 47</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [101] 19 9 7 9 63 52 41 67 5 33 21 20 42 4 17 35 66 19 34 37 18 23 33 8 7</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [126] 51 41 60 38 2 67 58 10 42 38 1 29 49 10 22 46 67 1 3 39 61 27 32 5 63</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [151] 12 16 3 53 7 49 31 23 11 22 29 37 30 45 32 35 45 1 56 46 23 18 49 64 30</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [176] 27 8 1 6 32 9 10 18 12 20 37 46 49 9 24 10 67 57 8 55 48 62 65 31 61</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] FALSE TRUE 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> [13] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE 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> [73] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</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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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></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;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-06 24D393 20 F Clinical B_ESCHR_COLI R NA NA NA </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-06-19 402950 53 F Clinical B_STPHY_HMNS R NA S NA </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
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||||
@ -245,16 +247,16 @@
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_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;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 534091 2015-02-15 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 968584 2005-12-29 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 419568 2014-10-19 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 291882 2010-05-01 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> A97263 2013-11-23 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 192353 2010-04-05 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 189363 2004-06-22 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 422833 2017-03-21 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34429 2011-01-02 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C11627 2014-09-11 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 023456 2012-11-24 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A79917 2016-05-21 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 257844 2011-05-22 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F50462 2008-05-11 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3CF3C4 2006-06-26 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E29972 2014-11-22 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 406502 2004-02-29 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D10538 2016-08-13 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 336698 2006-07-02 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> DF7736 2014-02-19 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">%>%</a></span></span></span>
|
||||
@ -266,19 +268,19 @@
|
||||
<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">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [182]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<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;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2015-02-15 534091 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2005-12-29 968584 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2014-10-19 419568 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2010-05-01 291882 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2013-11-23 A97263 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-04-05 192353 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-06-22 189363 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2017-03-21 422833 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2011-01-02 C34429 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2014-09-11 C11627 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [178]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<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;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2012-11-24 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2016-05-21 A79917 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-05-22 257844 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2008-05-11 F50462 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-06-26 3CF3C4 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2014-11-22 E29972 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-02-29 406502 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2016-08-13 D10538 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-07-02 336698 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2014-02-19 DF7736 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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">%>%</a></span></span></span>
|
||||
@ -293,9 +295,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 124 14 54 72</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 48 13 33 39</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 9 9</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 119 14 54 79</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 48 12 32 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 11 6 9 10</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>
|
||||
@ -325,19 +327,19 @@
|
||||
<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">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [190]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 534091 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 968584 B_PSDMN_AERG Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 419568 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 291882 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> A97263 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 192353 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 189363 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 422833 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34429 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C11627 B_STRPT_GRPC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [185]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 023456 B_PROTS_MRBL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A79917 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 257844 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F50462 B_STPHY_CONS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3CF3C4 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E29972 B_STPHY_HMNS Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 406502 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D10538 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 336698 B_NESSR_SICC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> DF7736 B_STRPT_PYGN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
|
||||
Reference in New Issue
Block a user