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Built site for AMR: 1.8.2.9047@d2edcf5
This commit is contained in:
github-actions
@ -177,41 +177,39 @@
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 45 29 45 57 14 40 18 59 22 11 17 11 1 44 60 54 15 38 11 21 17 55 46 57 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 53 5 57 3 28 45 20 15 38 16 60 20 25 24 28 63 10 4 9 19 17 56 34 19 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 8 38 62 51 62 7 36 57 14 46 54 58 44 37 59 57 7 6 46 9 10 8 60 54 17</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 21 5 49 50 8 9 39 8 52 20 30 3 14 54 13 36 47 2 59 18 56 18 17 41 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 58 22 53 26 43 29 53 42 25 53 61 37 2 1 55 62 61 32 27 39 12 7 62 10 30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 55 9 18 25 41 7 11 2 58 31 48 56 5 58 5 61 63 20 59 34 15 44 55 60 37</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 5 15 27 14 33 25 38 55 55 60 7 48 2 32 54 12 54 22 51 42 52 36 31 56 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 52 11 37 42 1 4 3 43 42 16 52 25 49 52 17 5 23 31 20 21 26 35 45 49 28</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 47 62 48 9 37 56 39 32 57 43 62 17 55 10 54 45 14 28 42 56 60 34 7 29 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 44 55 6 55 36 5 43 8 32 42 31 58 8 33 1 50 27 20 13 2 60 15 59 11 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 56 58 6 41 56 47 21 11 42 59 1 24 46 38 30 4 41 11 24 31 53 36 11 9 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 51 20 13 40 21 44 22 36 50 23 2 52 18 54 59 25 62 52 59 35 49 41 24 17 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 45 3 19 56 16 44 6 53 16 46 47 60 28 1 54 17 27 58 10 29 27 54 43 27 54</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 51 9 55 8 33 22 19 61 47 37 60 62 25 32 49 13 8 46 1 31 8 2 13 5 37</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 12 55 32 25 13 46 19 48 47 61 21 1 1 59 4 8 19 49 40 32 8 60 13 10 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 40 38 26 20 4 8 15 22 56 58 16 8 55 14 10 29 12 61 11 48 42 18 46 60 20</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-30 218912 76 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-22 FD8039 75 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-15 C42193 84 M ICU B_STPHY_HMNS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-23 F35553 51 M ICU B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
||||
<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>
|
||||
<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>
|
||||
@ -247,16 +245,16 @@
|
||||
<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> 255339 2013-07-22 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 942999 2009-02-17 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 963927 2013-07-04 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 7D5503 2016-05-30 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 990867 2005-08-16 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> C04744 2012-04-10 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 14D826 2006-09-14 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B77047 2016-12-03 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 005088 2007-08-22 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D65308 2004-11-03 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A97263 2013-11-23 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 3D2C93 2017-12-13 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 919B60 2013-12-31 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EB1709 2003-12-27 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 394307 2011-02-24 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 964129 2016-06-17 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 13DF24 2011-08-14 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 451000 2009-08-29 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34980 2016-06-28 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 4C9760 2012-09-06 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>
|
||||
@ -268,19 +266,19 @@
|
||||
<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 [184]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [177]</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 2013-07-22 255339 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-02-17 942999 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2013-07-04 963927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2016-05-30 7D5503 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-08-16 990867 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2012-04-10 C04744 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2006-09-14 14D826 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2016-12-03 B77047 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-08-22 005088 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2004-11-03 D65308 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-11-23 A97263 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-12-13 3D2C93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2013-12-31 919B60 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-12-27 EB1709 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2011-02-24 394307 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2016-06-17 964129 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2011-08-14 13DF24 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2009-08-29 451000 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2016-06-28 C34980 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2012-09-06 4C9760 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>
|
||||
@ -295,9 +293,9 @@
|
||||
<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 120 14 54 74</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 54 13 37 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 10 10</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 105 15 51 69</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 60 12 36 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 12 6 11 12</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>
|
||||
@ -327,19 +325,19 @@
|
||||
<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 [194]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [188]</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> 255339 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 942999 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 963927 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 7D5503 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 990867 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> C04744 B_STRPT_EQNS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 14D826 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B77047 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 005088 B_SLMNL_ENTR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D65308 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A97263 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 3D2C93 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 919B60 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EB1709 B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 394307 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 964129 B_SERRT_MRCS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 13DF24 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 451000 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C34980 B_STRPT_PYGN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 4C9760 B_ESCHR_COLI Clinical 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