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Built site for AMR: 1.8.2.9084@86e28ba
This commit is contained in:
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="">1.8.2.9083</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9084</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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@ -182,39 +182,40 @@
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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>
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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] 60 32 64 53 16 36 44 56 18 28 21 26 16 25 28 61 21 23 43 13 34 13 43 44 47</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 55 65 65 19 65 7 41 20 49 53 19 44 57 33 51 6 33 22 32 36 46 62 55 38 56</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 59 7 25 63 36 29 10 13 31 27 28 54 11 25 31 17 59 48 23 30 54 36 27 63 24</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 9 25 11 17 50 41 49 56 27 21 12 48 37 48 5 15 18 20 22 11 41 12 43 43 13</span>
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<span class="r-out co"><span class="r-pr">#></span> [101] 49 39 55 20 10 64 43 50 14 43 47 60 40 26 32 3 41 26 59 35 44 61 24 18 42</span>
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<span class="r-out co"><span class="r-pr">#></span> [126] 36 41 41 54 1 1 53 8 29 45 2 59 60 48 53 35 30 41 63 58 46 18 53 61 9</span>
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<span class="r-out co"><span class="r-pr">#></span> [151] 30 10 14 4 7 62 62 39 30 27 54 29 24 60 40 41 63 6 42 21 25 23 19 15 52</span>
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<span class="r-out co"><span class="r-pr">#></span> [176] 8 54 36 11 43 10 33 56 30 2 45 23 1 57 64 65 22 31 35 10 25 15 2 34 53</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 35 62 35 6 5 61 64 22 27 58 10 64 57 60 29 58 21 9 15 3 46 19 32 23 55</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 5 58 29 21 36 62 41 18 12 20 41 62 6 38 26 37 41 33 35 22 15 20 61 4 19</span>
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<span class="r-out co"><span class="r-pr">#></span> [51] 25 41 51 48 50 44 11 42 10 57 45 2 27 16 53 35 41 62 28 54 36 12 7 39 5</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 12 58 19 14 63 30 28 10 8 54 17 46 30 53 32 14 31 30 17 46 16 39 59 48 52</span>
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<span class="r-out co"><span class="r-pr">#></span> [101] 49 1 12 57 33 37 51 12 22 13 27 16 60 36 9 64 10 33 2 42 40 4 24 15 60</span>
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<span class="r-out co"><span class="r-pr">#></span> [126] 31 63 49 2 43 45 53 53 38 48 38 39 48 60 61 12 4 27 37 37 27 28 56 34 28</span>
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<span class="r-out co"><span class="r-pr">#></span> [151] 47 11 14 58 24 54 64 16 59 15 7 31 45 23 10 32 21 61 43 21 14 38 58 13 14</span>
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<span class="r-out co"><span class="r-pr">#></span> [176] 12 1 59 24 23 60 6 19 7 5 3 7 32 37 24 54 24 52 24 39 15 58 32 9 14</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 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [13] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [121] TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [157] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE FALSE FALSE TRUE FALSE 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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<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> 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> 2002-08-14 785317 51 F ICU 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: #949494;"># A tibble: 2 × 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> 2002-10-11 871360 78 M Clinical B_STPHY_EPDR R NA S NA </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-11 D80753 74 F Outpatie… B_STPHY_CONS 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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||||
@ -250,16 +251,16 @@
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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> 305134 2016-10-28 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 0DBB93 2009-05-08 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> F50400 2017-09-08 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> AC8303 2014-10-20 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 425433 2005-07-11 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AB0003 2010-04-08 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 452218 2012-05-04 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 904640 2015-11-03 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 968584 2006-01-11 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 773560 2008-05-08 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 387C40 2010-12-06 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 6FC260 2017-06-07 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 829641 2011-01-03 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 914520 2003-07-31 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 114570 2003-04-08 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 612042 2017-03-15 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> C80762 2017-12-21 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 650870 2007-09-10 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> CD4354 2009-02-19 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C6F894 2016-07-11 C 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>
|
||||
@ -271,19 +272,19 @@
|
||||
<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 [186]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [179]</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> ICU 2016-10-28 305134 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2009-05-08 0DBB93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2017-09-08 F50400 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-10-20 AC8303 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-07-11 425433 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-04-08 AB0003 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-05-04 452218 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-11-03 904640 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2006-01-11 968584 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2008-05-08 773560 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2010-12-06 387C40 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-06-07 6FC260 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-01-03 829641 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2003-07-31 914520 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2003-04-08 114570 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2017-03-15 612042 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2017-12-21 C80762 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2007-09-10 650870 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2009-02-19 CD4354 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2016-07-11 C6F894 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>
|
||||
@ -298,9 +299,9 @@
|
||||
<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 110 14 53 71</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 62 12 38 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 14 9 12 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 106 14 52 73</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 60 12 36 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 13 9 13 13</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>
|
||||
@ -330,19 +331,19 @@
|
||||
<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 [195]</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> 305134 B_PROTS_VLGR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 0DBB93 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> F50400 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> AC8303 B_STPHY_HMLY Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 425433 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AB0003 B_STRPT_ANGN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 452218 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 904640 B_PROTS_MRBL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 968584 F_CANDD_ALBC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 773560 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [192]</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> 387C40 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 6FC260 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 829641 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 914520 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 114570 B_STRPT_GRPA ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 612042 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> C80762 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 650870 B_ENTRBC_CLOC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> CD4354 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C6F894 B_STPHY_AURS 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