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Built site for AMR: 1.8.2.9098@19fd0ef
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="">1.8.2.9096</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9098</small>
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|
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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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@ -182,41 +182,41 @@
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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] 9 46 28 50 35 57 44 17 9 56 15 7 12 51 27 22 32 14 29 44 55 54 12 3 15</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [26] 46 6 5 47 12 40 5 51 16 40 46 26 37 1 50 3 23 13 11 19 25 54 36 49 15</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 63 19 55 54 5 62 11 55 6 50 60 44 52 45 57 40 10 46 19 2 6 2 12 19 2</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [76] 37 7 16 47 59 49 24 57 19 25 48 43 28 59 56 59 41 4 23 25 58 56 32 43 34</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [101] 33 42 33 17 7 48 12 50 48 15 49 8 34 59 25 49 29 35 61 58 23 63 59 25 40</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [126] 57 46 20 21 26 16 12 16 7 27 8 21 38 48 8 26 52 51 41 24 42 60 11 52 31</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [151] 36 26 24 54 20 53 23 61 52 57 25 55 43 63 30 38 47 60 5 62 3 61 5 27 14</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [176] 37 12 25 63 54 30 39 1 15 55 5 55 34 38 63 20 18 24 31 12 32 20 2 7 32</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 9 29 29 17 30 21 4 56 31 35 18 50 62 7 28 28 57 37 53 46 15 23 14 39 42</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [26] 46 20 62 29 54 18 54 1 61 3 12 6 8 9 43 24 1 61 37 11 42 28 36 12 8</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 26 61 55 60 4 19 30 7 20 9 13 57 9 59 47 8 17 1 64 8 2 4 60 7 34</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [76] 61 44 20 61 55 7 2 32 33 18 6 18 11 7 10 18 5 3 44 23 54 31 18 4 19</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [101] 25 17 7 41 43 17 55 21 30 61 11 16 14 57 52 41 40 23 43 60 37 26 12 12 4</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [126] 10 6 40 11 2 45 30 51 47 29 25 58 10 61 19 8 39 1 24 25 58 10 18 34 20</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [151] 63 43 57 51 60 41 36 64 4 61 55 22 19 27 53 64 51 15 55 23 22 36 45 57 48</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [176] 40 44 49 57 38 40 29 32 2 11 50 38 53 10 33 8 9 54 4 6 58 57 3 14 60</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>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] TRUE FALSE FALSE TRUE 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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||||
<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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_BCTRD_FRGL R NA NA R </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL 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> 2002-09-23 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-08-28 390178 57 M Clinical B_STRPT_SLVR S NA NA S </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</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: #BCBCBC;">3</span> 2002-07-24 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>,</span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>,</span></span>
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||||
@ -226,11 +226,12 @@
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MUP <sir>, RIF <sir></span></span>
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||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fl">60</span> <span class="op">*</span> <span class="fl">60</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span>episode_days <span class="op">=</span> <span class="fl">1</span> <span class="op">/</span> <span class="fl">24</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fl">60</span> <span class="op">*</span> <span class="fl">60</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> episode_days <span class="op">=</span> <span class="fl">1</span> <span class="op">/</span> <span class="fl">24</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -252,16 +253,16 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_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;"><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> F24801 2004-02-10 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 263940 2013-03-05 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E95747 2008-06-30 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 414858 2014-08-29 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 823896 2010-03-04 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 976813 2016-05-09 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 107DD1 2012-09-03 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 89F819 2005-11-27 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 89F578 2004-02-28 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 329C35 2016-04-03 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 822116 2004-02-24 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 144549 2009-09-01 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 982666 2009-09-06 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 5DF436 2006-01-04 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 023456 2009-11-02 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 725063 2007-06-07 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> FCC668 2002-10-14 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D28985 2015-12-21 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B26404 2010-01-02 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> F83217 2010-12-21 B 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>
|
||||
@ -273,19 +274,19 @@
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></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> ICU 2004-02-10 F24801 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2013-03-05 263940 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-06-30 E95747 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-08-29 414858 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-03-04 823896 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2016-05-09 976813 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-09-03 107DD1 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2005-11-27 89F819 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2004-02-28 89F578 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2016-04-03 329C35 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [183]</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 2004-02-24 822116 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-09-01 144549 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-09-06 982666 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2006-01-04 5DF436 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2009-11-02 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2007-06-07 725063 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2002-10-14 FCC668 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Outpatient 2015-12-21 D28985 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2010-01-02 B26404 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2010-12-21 F83217 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>
|
||||
@ -300,11 +301,10 @@
|
||||
<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 15 57 81</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 47 12 35 42</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 11 6 10 10</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 118 14 51 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 59 13 37 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 6 6</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>
|
||||
<span class="r-in"><span> <span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">x</span> <span class="op"><-</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>
|
||||
@ -321,9 +321,8 @@
|
||||
<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">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE</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>
|
||||
<span class="r-in"><span> <span class="co"># since you can now group on anything that seems relevant:</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>
|
||||
@ -333,18 +332,18 @@
|
||||
<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 [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> F24801 B_STRPT_GRPB ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 263940 B_STPHY_HMNS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E95747 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 414858 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 823896 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 976813 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 107DD1 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 89F819 B_CRYNB ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 89F578 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 329C35 B_ESCHR_COLI Clinical TRUE </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> 822116 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 144549 B_ENTRBC_CLOC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 982666 B_STRPT_DYSG Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 5DF436 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 023456 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 725063 B_STPHY_CONS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> FCC668 B_ACNTB ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D28985 B_ESCHR_COLI Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B26404 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> F83217 B_STPHY_CONS 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