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@@ -62,7 +62,7 @@ Principal component analysis for AMR
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reference/ab_from_text.html
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reference/add_custom_antimicrobials.html
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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="">1.8.2.9072</small>
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reference/add_custom_microorganisms.html
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<!DOCTYPE html>
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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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -133,7 +133,7 @@
</div>
<div class="ref-description section level2">
<p>With <code>add_custom_microorganisms()</code> you can add your own custom antimicrobial drug codes to the <code>AMR</code> package.</p>
<p>With <code>add_custom_microorganisms()</code> you can add your own custom microorganisms to the <code>AMR</code> package, such the non-taxonomic outcome of laboratory analysis.</p>
</div>
<div class="section level2">
@@ -195,10 +195,12 @@
<span class="r-in"><span><span class="co"># E. asburiae/cloacae is now a new microorganism:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacter asburiae/cloacae"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># its code:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CUSTOM_ENTRBC_A_C</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># all internal algorithms will work as well:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Ent asburia cloacae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacter asburiae/cloacae"</span>

22
reference/age.html
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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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -195,16 +195,16 @@
<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">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1972-04-12 50 50.71233 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1937-10-17 85 85.19726 62</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1956-07-07 66 66.47671 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1967-07-04 55 55.48493 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1962-01-28 60 60.91507 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1962-12-05 60 60.06301 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1961-03-12 61 61.79726 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1967-09-09 55 55.30137 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1967-01-22 55 55.93151 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1936-09-15 86 86.28493 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1941-07-04 81 81.48493 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1981-12-16 41 41.03288 18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1998-10-03 24 24.23562 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1944-10-01 78 78.24110 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1967-01-03 55 55.98356 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1953-07-10 69 69.46849 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-11-13 25 25.12329 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1951-12-30 70 70.99452 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1953-10-07 69 69.22466 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1966-07-15 56 56.45479 33</span>
</code></pre></div>
</div>
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2
reference/as.av.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/as.disk.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/as.mic.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/as.mo.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

22
reference/as.rsi.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-28 <span style="color: #949494;">13:24:25</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-28 <span style="color: #949494;">13:24:26</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-28 <span style="color: #949494;">13:24:26</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-28 <span style="color: #949494;">13:24:26</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-28 <span style="color: #949494;">13:24:27</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-28 <span style="color: #949494;">13:24:27</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-28 <span style="color: #949494;">13:24:28</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-28 <span style="color: #949494;">13:24:28</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-28 <span style="color: #949494;">13:24:28</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-28 <span style="color: #949494;">13:24:28</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-12-28 <span style="color: #949494;">14:09:48</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-28 <span style="color: #949494;">14:09:49</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-12-28 <span style="color: #949494;">14:09:49</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-12-28 <span style="color: #949494;">14:09:49</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-28 <span style="color: #949494;">14:09:50</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²​mo_input, ³​guideline</span></span>

2
reference/atc_online.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/av_from_text.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/av_property.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/availability.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/bug_drug_combinations.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/count.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</small>
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2
reference/custom_eucast_rules.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/dosage.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/eucast_rules.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</small>
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2
reference/example_isolates.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/example_isolates_unclean.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/first_isolate.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/g.test.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

131
reference/get_episode.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -182,40 +182,39 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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">#&gt;</span> [1] 10 6 35 25 25 48 41 23 28 27 51 26 47 12 1 52 2 16 34 47 57 66 62 34 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 27 12 12 59 49 15 13 51 14 14 5 13 10 66 34 65 26 44 51 5 27 50 42 58 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 9 53 51 65 24 8 13 50 1 40 31 7 62 32 40 28 19 55 34 36 24 7 28 60 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 10 12 41 43 58 64 57 60 8 9 47 39 30 52 4 67 61 55 13 37 4 57 32 44 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 27 10 8 56 15 6 66 67 54 38 34 17 3 64 49 18 50 65 40 60 3 49 10 17 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 12 12 51 4 41 60 12 63 18 9 45 11 47 21 37 65 61 65 57 5 58 57 12 28 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 58 25 66 60 24 8 29 58 39 30 60 45 23 50 12 38 55 63 20 43 63 2 36 31 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 7 10 16 61 33 20 18 44 35 26 40 43 14 22 33 42 28 46 40 39 2 42 32 7 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 55 22 2 7 13 47 45 36 28 21 45 31 46 9 22 42 6 25 28 48 35 10 11 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 23 58 59 44 57 34 40 26 33 45 51 39 7 20 38 35 6 18 32 1 1 46 10 9 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 37 41 5 36 8 58 40 50 58 59 57 9 35 59 51 16 48 57 33 2 39 35 58 20 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 20 4 5 18 2 26 25 8 20 7 33 40 19 28 44 49 28 38 15 27 57 22 43 27 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 25 36 32 26 38 27 16 3 32 56 10 51 8 9 40 30 6 29 51 2 53 8 53 33 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 28 18 6 19 50 10 51 15 53 28 38 20 38 42 12 49 33 24 58 36 26 52 5 24 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 55 37 11 47 22 44 12 57 6 16 21 54 45 36 15 49 12 4 53 38 6 60 13 47 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 36 30 14 18 17 10 23 10 56 55 18 1 19 19 24 14 34 45 50 54 2 27 12 15 45</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">#&gt;</span> [1] TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [145] TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [181] TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE TRUE FALSE FALSE FALSE TRUE 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">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> <span style="color: #BCBCBC;">2</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">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-19 402950 53 F Clinical B_STPHY_HMNS R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -251,16 +250,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: condition [3]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 189363 2004-06-22 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F35553 2003-09-05 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2E6911 2010-06-05 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 451990 2008-03-22 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 192790 2008-02-15 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B43936 2013-05-16 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 5B78D5 2011-09-19 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 179451 2007-09-15 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 329273 2008-10-27 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B12441 2008-09-21 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 324415 2015-10-03 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 671620 2016-12-04 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 403631 2007-07-31 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F30196 2002-04-14 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A73011 2003-08-13 C FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F63168 2005-02-25 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C34429 2014-12-15 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 658640 2014-05-30 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 687590 2011-10-29 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 408807 2009-05-07 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</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">%&gt;%</a></span></span></span>
@@ -272,19 +271,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [183]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [179]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2004-06-22 189363 2 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-09-05 F35553 2 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2010-06-05 2E6911 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2008-03-22 451990 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Outpatient 2008-02-15 192790 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2013-05-16 B43936 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2011-09-19 5B78D5 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2007-09-15 179451 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-10-27 329273 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-09-21 B12441 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2015-10-03 324415 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2016-12-04 671620 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-07-31 403631 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Outpatient 2002-04-14 F30196 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2003-08-13 A73011 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2005-02-25 F63168 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2014-12-15 C34429 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2014-05-30 658640 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2011-10-29 687590 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2009-05-07 408807 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</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">%&gt;%</a></span></span></span>
@@ -299,9 +298,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 117 15 54 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 56 12 36 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 6 9 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 118 14 52 75</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 51 12 34 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 6 11 11</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>
@@ -331,19 +330,19 @@
<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">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [192]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [188]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 189363 B_STPHY_AURS Clinical FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F35553 B_ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2E6911 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 451990 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 192790 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B43936 B_BCTRD_FRGL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 5B78D5 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 179451 B_ESCHR_COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 329273 B_STRPT_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B12441 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 324415 B_PROTS_MRBL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 671620 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 403631 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F30196 B_STRPT_GRPB Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A73011 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F63168 B_STRPT_EQUI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C34429 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 658640 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 687590 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 408807 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</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>

2
reference/ggplot_pca.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/ggplot_rsi.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/guess_ab_col.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/index.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/intrinsic_resistant.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/italicise_taxonomy.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/join.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/key_antimicrobials.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

6
reference/kurtosis.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -172,9 +172,9 @@
<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">#&gt;</span> [1] 3.008528</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.04852</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">#&gt;</span> [1] -0.0002890877</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06879899</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

2
reference/mdro.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">

78
reference/mean_amr_distance.html
View File

@@ -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="">1.8.2.9072</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9073</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">
@@ -200,10 +200,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 8 4 0.025 0.25 0.025 2 256 128 0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 0.0625 0.0625 64 64 2 &gt;=256 &gt;=256 0.125 0.0625</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.1267814234 0.3751651897 0.1872611313 -1.1885588733 -0.5643551025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -1.1885588733 -0.0006429272 1.3146854818 1.1267814234 -1.1885588733</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.44345719 -1.02187960 -1.02187960 0.90619512 0.90619512 -0.05784224</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.29181006 1.29181006 -0.82907213 -1.02187960</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
@@ -213,38 +213,38 @@
<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">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.5 16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 &lt;=1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &gt;=1 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 0.25 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 0.25 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.5 &lt;=1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 &lt;=1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.5 16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 16 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.125 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &lt;=0.25 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 &lt;=0.25 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.25 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 &gt;=2 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=2 1 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 &gt;=2 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">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.0433511 -0.1293101 0.3461827 -0.2821777 -0.2881837 -0.1918269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4613005 0.4590383 -0.3164093 -0.1793638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.81284429 -0.28991150 -1.03511883 -0.22702202 0.11273878 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.85671083 -0.80055308 0.04737875 0.41019401</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.0625 &lt;=1 8 -0.4613005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 8 0.125 16 1 -0.3164093</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 1 0.25 8 4 -0.2881837</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 2 0.25 4 4 -0.2821777</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.5 &lt;=1 1 -0.1918269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.125 4 4 -0.1793638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 &lt;=1 2 -0.1293101</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &gt;=1 2 8 0.3461827</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 16 0.5 16 2 0.4590383</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.5 16 8 1.0433511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 4 &lt;=0.25 1 2 -1.03511883</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 0.5 2 1 -0.80055308</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 0.5 2 2 -0.28991150</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2 -0.22702202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &lt;=2 1 &gt;=4 4 0.04737875</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 &lt;=0.25 &gt;=4 4 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 &lt;=0.25 &gt;=4 4 0.11273878</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 &gt;=2 2 2 0.41019401</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &gt;=64 1 &gt;=4 4 0.81284429</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 32 &gt;=2 &gt;=4 4 0.85671083</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>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -256,17 +256,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 &gt;=1 2 8 0.3461827 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 16 0.5 16 2 0.4590383 0.1128555</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B 16 0.5 &lt;=1 2 -0.1293101 0.4754929</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J 8 0.125 4 4 -0.1793638 0.5255465</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F 32 0.5 &lt;=1 1 -0.1918269 0.5380096</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D 2 0.25 4 4 -0.2821777 0.6283605</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 1 0.25 8 4 -0.2881837 0.6343665</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I 8 0.125 16 1 -0.3164093 0.6625920</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 32 0.5 16 8 1.0433511 0.6971683</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G 8 &lt;=0.0625 &lt;=1 8 -0.4613005 0.8074832</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 4 &lt;=0.25 1 2 -1.03511883 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 H 8 0.5 2 1 -0.80055308 0.2345657</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B 16 0.5 2 2 -0.28991150 0.7452073</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 32 &gt;=2 &lt;=0.5 2 -0.22702202 0.8080968</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I &lt;=2 1 &gt;=4 4 0.04737875 1.0824976</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 16 &lt;=0.25 &gt;=4 4 0.11273878 1.1478576</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F 16 &lt;=0.25 &gt;=4 4 0.11273878 1.1478576</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J &gt;=64 &gt;=2 2 2 0.41019401 1.4453128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A &gt;=64 1 &gt;=4 4 0.81284429 1.8479631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G 32 &gt;=2 &gt;=4 4 0.85671083 1.8918297</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">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -10,7 +10,7 @@
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@@ -183,43 +183,42 @@
<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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 &lt;=0.001 1 16 2 0.025 0.005 0.25 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 8 0.002 &lt;=0.001 0.025 256 &lt;=0.001 8 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 16 4 1 1 0.25 0.005 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.5 4 1 &lt;=0.001 0.125 16 256 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125 128 4 0.5 16 0.0625 4 0.005 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.001 8 64 64 4 0.005 2 </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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 45 50 48 45 18 18 19 9 37 23 45 35 18 34 47 36 31 12 21 7 42 30 9 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 28 48 25 23 10 14 47 37 13 14 7 23 15 21 7 11 41 41 7 40 30 47 26 11</span>
<span class="r-in"><span><span class="fu">random_rsi</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">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I I I I R R S S I R R I I R R R I S S R I I S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R I S I R R R R R I I S I S S S R R R R I S 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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 0.25 &lt;=0.002 8 0.0625 0.125 128 4 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2 4 0.005 16 &lt;=0.002 1 0.005 0.25 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.01 0.025 2 0.125 64 &lt;=0.002 &lt;=0.002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 1 0.0625 2 64 1 0.5 32 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.025 16 0.01 0.005 0.5 0.025 0.0625 16 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.005 &lt;=0.001 0.01 0.002 32 4 2 </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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 8 1 16 2 8 16 &lt;=0.5 2 1 2 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &lt;=0.5 1 8 &lt;=0.5 1 16 4 16 &lt;=0.5 4 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=64 32 32 2 16 2 &gt;=64 32 4 &gt;=64 1 32 32 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] &gt;=64 4 8 2 4 &gt;=64 16 4 1 4 </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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 2 4 0.5 0.125 0.0625 &lt;=0.025 2 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.025 2 0.5 1 4 0.25 &lt;=0.025 0.25 &lt;=0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 0.125 0.0625 &lt;=0.025 2 1 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 8 16 1 2 8 0.25 8 8 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 1 0.0625 8 16 8 0.5 0.025 4 1 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 0.025 2 0.5 8 </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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 12 42 49 11 15 16 24 16 42 48 15 48 13 45 47 45 39 48 36 11 40 50 42 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 18 36 26 41 46 31 9 9 33 20 47 10 50 29 49 25 17 48 8 37 41 42 31 42</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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 13 11 16 14 15 11 13 14 12 13 11 12 14 13 11 16 15 12 15 15 13 12 14 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 15 14 14 11 12 16 12 15 17 13 15 12 11 12 17 16 17 17 15 15 16 11 15 15</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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 16 27 26 25 23 23 20 19 15 22 23 21 22 15 17 24 21 19 21 27 25 16 15 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 19 26 15 15 19 15 20 26 20 26 21 23 26 27 21 15 26 24 26 15 17 20 18 23</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@@ -171,7 +171,7 @@ 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">#&gt;</span> [1] -0.01851306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.005679332</span>
</code></pre></div>
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