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@ -205,16 +205,16 @@
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<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1977-02-20 45 45.98356 22</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1950-04-11 72 72.84658 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1944-09-13 78 78.42192 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1995-08-12 27 27.50959 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1935-10-04 87 87.36438 64</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1989-07-22 33 33.56712 10</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1968-04-20 54 54.82192 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1940-09-20 82 82.40274 59</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1943-05-17 79 79.74795 56</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1935-05-19 87 87.74247 64</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1936-04-02 86 86.87123 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1952-02-14 71 71.00000 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1944-06-12 78 78.67671 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1993-06-22 29 29.64932 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1956-05-01 66 66.79178 43</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1954-09-25 68 68.38904 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1985-02-09 38 38.01370 14</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1991-05-30 31 31.71233 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1933-03-14 89 89.92329 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1982-02-26 40 40.96712 17</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></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>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-02-14 <span style="color: #949494;">09:46:41</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-02-14 <span style="color: #949494;">09:46:41</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-02-14 <span style="color: #949494;">09:46:41</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-02-14 <span style="color: #949494;">09:46:40</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-02-14 <span style="color: #949494;">09:46:36</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-02-14 <span style="color: #949494;">15:07:38</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-02-14 <span style="color: #949494;">15:07:37</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-02-14 <span style="color: #949494;">15:07:37</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-02-14 <span style="color: #949494;">15:07:36</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-02-14 <span style="color: #949494;">15:07:30</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table <chr>, method <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr>, ab_considered <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># mo_considered <lgl>, breakpoint_S <lgl>, breakpoint_R <lgl>,</span></span>
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
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|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
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|
@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -12,7 +12,7 @@
|
||||
|
||||
<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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
@ -192,31 +192,29 @@
|
||||
<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">100</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 29 3 41 20 36 3 13 26 3 7 46 20 18 25 41 32 38 19 12 10 37 17 16 7 18</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 27 10 13 45 2 22 44 19 9 2 14 18 11 39 40 8 9 7 6 19 3 47 39 44 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 43 25 8 13 28 30 15 40 9 42 3 12 16 1 18 37 26 10 44 41 15 21 26 1 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 26 34 46 24 4 41 21 23 5 12 35 15 10 12 43 1 43 33 11 41 45 31 12 33 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 35 25 44 41 29 17 16 4 49 30 12 28 37 49 43 47 11 44 35 3 1 19 11 18 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 45 23 1 3 33 5 26 48 49 2 48 10 39 14 10 28 8 4 27 9 42 18 16 47 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 7 24 8 9 36 31 7 34 18 39 32 29 10 23 2 13 44 22 15 40 47 17 38 48 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 16 21 21 21 20 15 41 6 49 24 31 6 7 30 4 20 46 19 32 1 39 48 3 45 27</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE</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: 5 × 46</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> 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;"><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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-04 304347 62 M Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-16 762305 87 F Clinical B_BCTRD_FRGL R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2003-01-08 783073 83 M Clinical B_STPHY_CONS R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
@ -254,16 +252,16 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [96]</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> 022060 2004-05-04 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 077922 2009-08-18 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 080086 2007-10-26 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0E2483 2007-05-29 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 122506 2007-08-10 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 125492 2016-05-13 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 156730 2012-04-12 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 161740 2005-06-21 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 16DC39 2015-11-19 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 16F0F7 2010-01-17 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 023456 2002-02-05 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 023456 2011-04-25 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 032343 2003-06-09 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 047634 2004-06-28 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 067927 2002-01-13 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 078381 2014-07-17 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 0C0688 2014-09-05 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 0DBF93 2015-12-03 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-08-10 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 0E2483 2008-07-22 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</span></span>
|
||||
<span class="r-in"><span></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>
|
||||
@ -277,19 +275,19 @@
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</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: 100 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [96]</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;"><int></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 2004-05-04 022060 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-08-18 077922 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-10-26 080086 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2007-08-10 122506 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2016-05-13 125492 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-04-12 156730 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2005-06-21 161740 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2015-11-19 16DC39 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2010-01-17 16F0F7 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2002-02-05 023456 2 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2011-04-25 023456 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2003-06-09 032343 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2004-06-28 047634 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2002-01-13 067927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-07-17 078381 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2015-12-03 0DBF93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-07-22 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2007-08-10 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</span></span>
|
||||
<span class="r-in"><span></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>
|
||||
@ -305,9 +303,9 @@
|
||||
<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 57 13 34 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 33 10 22 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 5 4 5 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 61 14 40 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 31 10 24 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 4 4 4 4</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>
|
||||
@ -325,7 +323,7 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<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-out co"><span class="r-pr">#></span> [1] FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</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>
|
||||
@ -336,19 +334,19 @@
|
||||
<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: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [100]</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> C34429 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 304347 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 125492 B_STRPT_DYSG ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> CB6026 B_PSDMN_AERG Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 835073 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 762305 B_BCTRD_FRGL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 968584 F_CANDD_ALBC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 16F0F7 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> F35553 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 399817 B_CTRBC_FRND Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 187841 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> AB0003 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 0DBF93 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0C0688 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B61944 B_STPHY_CONS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E31163 B_STPHY_CONS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 868305 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 032343 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> C13048 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 023456 B_PROTS_MRBL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
@ -182,9 +182,9 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.038876</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3.020372</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.02698212</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.06805045</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
@ -201,30 +201,30 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">sir</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R S R R I I I R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] I S S I R S S R S R</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833 -0.9486833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 -0.9486833 0.9486833 0.9486833</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 -0.621059 1.449138 -0.621059 -0.621059</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 1.449138</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 2 0.001 2 0.025 256 0.025 64 0.025 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 4 1 64 0.01 4 0.025 0.002 0.5 >=128</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.12797444 0.41517764 -1.57018523 0.41517764 -0.72941183 1.68253251</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.72941183 1.32043112 -0.72941183 0.05307625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.41273419 0.58164698 0.24829965 1.24834166 -0.85905624 0.58164698</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.63872564 -1.24606052 0.08162598 1.41501533</span>
|
||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.12797444 0.41517764 -1.57018523 0.41517764 -0.72941183 1.68253251</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.72941183 1.32043112 -0.72941183 0.05307625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.41273419 0.58164698 0.24829965 1.24834166 -0.85905624 0.58164698</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.63872564 -1.24606052 0.08162598 1.41501533</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 22 47 8 19 40 38 47 19 7 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 40 31 10 19 43 48 7 32 9 29</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.2169449 1.3326617 -1.0847246 -0.4028977 0.8987718 0.7748033</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.3326617 -0.4028977 -1.1467089 -1.0847246</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.8882407 0.2826221 -1.1304882 -0.5248695 1.0901136 1.4265685</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.3323611 0.3499130 -1.1977792 0.1480401</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||
@ -234,22 +234,22 @@
|
||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A S 26 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 20 0.25 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 23 8 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D R 30 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 0.25 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 8 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 16 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H R 26 0.25 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J I 17 1 <=0.25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 26 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B S 21 0.5 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C I 20 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 0.25 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E R 25 1 0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 17 0.25 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 1 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 19 >=4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 18 0.25 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J S 18 2 2</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.08488745 -0.47455213 -0.28834263 0.92954003 0.44478586 0.07490685</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.82469031 -0.04972854 -0.23217610 -1.14423619</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.91414006 -0.17605318 0.09856581 -0.54009185 0.24439443 -0.45907292</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 0.50845312 0.40655103 -0.70032567 -0.29656083</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
@ -265,17 +265,17 @@
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C I 23 8 1 -0.28834263 0.00000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 I R 20 0.25 4 -0.23217610 0.05616652</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B S 20 0.25 16 -0.47455213 0.18620951</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A S 26 1 8 -0.08488745 0.20345517</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 H R 26 0.25 2 -0.04972854 0.23861409</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F R 23 8 0.5 0.07490685 0.36324947</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E R 31 0.25 8 0.44478586 0.73312849</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J I 17 1 <=0.25 -1.14423619 0.85589357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 G R 31 16 2 0.82469031 1.11303293</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D R 30 4 16 0.92954003 1.21788265</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C I 20 1 16 0.09856581 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 E R 25 1 0.5 0.24439443 0.1458286</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B S 21 0.5 8 -0.17605318 0.2746190</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H I 19 >=4 16 0.40655103 0.3079852</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J S 18 2 2 -0.29656083 0.3951266</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 G I 29 1 8 0.50845312 0.4098873</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 F I 17 0.25 16 -0.45907292 0.5576387</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 D S 23 0.25 2 -0.54009185 0.6386577</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I S 18 0.25 4 -0.70032567 0.7988915</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A R 26 1 8 0.91414006 0.8155742</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="co"># support for groups</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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">
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
|
||||
|
||||
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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9124</small>
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@ -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="">1.8.2.9124</small>
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Before Width: | Height: | Size: 25 KiB After Width: | Height: | Size: 25 KiB |
Before Width: | Height: | Size: 26 KiB After Width: | Height: | Size: 26 KiB |
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Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 37 KiB |
Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 37 KiB |
Before Width: | Height: | Size: 36 KiB After Width: | Height: | Size: 36 KiB |
Before Width: | Height: | Size: 36 KiB After Width: | Height: | Size: 38 KiB |
Before Width: | Height: | Size: 53 KiB After Width: | Height: | Size: 53 KiB |
Before Width: | Height: | Size: 27 KiB After Width: | Height: | Size: 26 KiB |
@ -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="">1.8.2.9124</small>
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9124</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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@ -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="">1.8.2.9124</small>
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@ -193,42 +193,43 @@
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.002 4 0.125 0.25 0.25 4 1 1 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 1 64 2 0.005 0.005 0.25 0.002 0.005 0.25 0.0625</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 1 256 64 0.005 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 256 256 1 4 32 0.002 256 0.5 0.001 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 2 0.5 0.002 0.25 64 0.001 8 1 0.025 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.0625 4 0.025 8 0.5 </span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 20 44 20 18 7 41 37 11 47 40 41 49 38 12 34 33 20 22 32 27 35 48 48 24 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 45 39 38 39 45 40 12 49 22 43 44 20 18 8 50 40 49 22 15 22 38 45 12 49 41</span>
|
||||
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I I R S I R R R S I S I I I S R S R S I S R R S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R R S I I S R R I I R S I S I I I I I I S I S R I</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] >=32 0.002 0.25 0.001 4 1 0.25 0.005 0.025 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 16 0.25 0.001 4 0.025 0.0625 0.5 8 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 1 0.002 8 0.5 0.001 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.01 0.0625 0.005 <=0.001 1 <=0.001 1 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.5 0.5 2 16 16 8 0.0625 32 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] <=0.001 4 0.002 0.25 0.005 0.0625 0.025 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2 >=32 8 >=32 16 >=32 16 4 1 2 16 1 1 >=32 >=32</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] 16 >=32 1 >=32 >=32 8 1 16 4 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.25 >=32 0.25 1 4 1 16 8 8 8 0.25 1 0.25 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] 2 2 4 8 >=32 0.25 >=32 >=32 >=32 0.5 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=0.125 8 <=0.125 2 1 1 0.25 1 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.125 2 2 1 0.25 1 4 1 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] <=0.125 0.5 <=0.125 2 0.25 2 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 2 1 0.5 0.25 0.125 0.5 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] 1 0.5 1 0.5 1 1 2 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] 0.125 0.25 0.125 0.5 0.5 0.25 <=0.0625 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 2 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 49 18 23 28 48 32 8 40 13 41 15 47 24 10 42 41 33 33 23 49 49 30 22 49 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 38 43 19 13 42 30 49 18 45 41 11 27 48 9 34 45 49 48 10 11 43 11 46 47 47</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 14 14 13 17 14 11 13 17 16 16 12 13 13 17 14 16 15 14 17 15 12 15 12 13 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 15 16 17 11 12 15 14 14 16 15 14 15 15 14 14 12 11 12 17 14 16 12 14 14</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 21 25 26 18 15 19 26 18 26 20 21 23 23 27 26 26 18 27 27 22 26 16 25 15 19</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 18 27 20 17 17 16 23 17 15 20 25 16 16 21 26 18 22 20 24 18 26 21 20 19 18</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
@ -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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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|
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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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|
@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<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="">1.8.2.9124</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</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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@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.06345232</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0002057774</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
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@ -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="">1.8.2.9124</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9125</small>
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