mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR: 1.8.1.9026@e05d036
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9021</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -82,11 +82,6 @@
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
<a class="dropdown-item" href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
Other: benchmarks
|
||||
</a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="active nav-item">
|
||||
@ -182,41 +177,40 @@
|
||||
<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] 63 42 61 46 22 21 21 10 46 12 31 47 53 64 9 27 12 7 30 25 15 61 52 20 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 46 53 39 38 54 61 58 12 58 39 21 27 35 66 46 59 57 13 43 30 29 60 51 25 35</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 22 4 56 20 5 18 18 22 9 21 50 9 58 38 59 44 46 11 41 55 55 5 14 56 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 53 63 33 20 5 31 32 10 1 51 46 2 28 24 40 10 13 26 55 12 49 54 16 43 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 51 37 60 27 49 23 42 63 5 60 7 23 4 37 47 22 52 45 65 56 11 38 17 36 12</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 9 47 25 14 1 56 38 66 42 53 19 51 10 34 16 11 15 62 31 40 22 63 49 32 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 45 6 48 5 58 57 7 56 46 13 58 65 15 21 7 42 8 5 6 6 28 29 4 26 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 3 56 3 60 61 63 63 56 65 16 21 40 57 23 16 47 58 61 21 32 9 60 3 17 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 6 17 60 34 7 61 19 35 61 38 26 59 25 61 25 20 50 2 20 5 53 35 67 48 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 11 17 20 59 66 54 26 60 44 48 20 12 23 37 4 5 36 21 28 59 20 44 11 60 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 6 12 16 16 62 40 4 17 64 52 33 20 3 1 55 46 12 12 30 64 22 8 2 30 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 28 61 31 52 63 35 15 7 45 51 65 41 36 33 14 53 18 40 12 42 55 2 15 14 38</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 23 9 9 23 22 58 3 26 20 6 1 68 43 39 24 46 12 40 56 29 39 1 8 59 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 57 14 64 65 37 41 42 37 20 24 32 59 14 61 52 10 13 59 18 24 40 52 62 30 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 10 35 65 61 10 16 20 4 53 16 24 47 2 67 27 58 64 1 11 62 12 40 47 1 20</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 22 54 21 29 11 23 59 61 40 39 42 14 14 17 66 17 2 52 23 29 2 68 24 46 14</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 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE TRUE TRUE 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 FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE 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 TRUE TRUE FALSE TRUE FALSE FALSE 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 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </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;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-18 B TRUE FALSE FALSE 30 M 012595 B_CRYNB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-23 B TRUE FALSE FALSE 51 M F35553 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-06-04 B TRUE FALSE FALSE 78 M 082413 B_STRPT_PNMN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-06-06 D FALSE TRUE FALSE 20 F 24D393 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,</span></span>
|
||||
@ -224,7 +218,6 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>, and …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `colnames()` to see all variable names</span></span>
|
||||
<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 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>
|
||||
|
||||
Reference in New Issue
Block a user