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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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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="">1.8.2.9037</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9038</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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@ -303,14 +303,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5688204 0.6218738</span>
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<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
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<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span><span class="op">)</span></span></span>
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<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5650148 0.6255670</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># determines %S+I:</span></span></span>
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<span class="r-in"><span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4044444</span>
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<span class="r-in"><span><span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
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<span class="r-in"><span> ab_result <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> ab_result <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.3781262 0.4311796</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># be more specific</span></span></span>
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@ -328,14 +330,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<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>
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> r <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="op">)</span> <span class="co"># n_rsi works like n_distinct in dplyr, see ?n_rsi</span></span></span>
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<span class="r-in"><span> </span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ward r n</span>
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@ -344,7 +344,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.190 447</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 93</span>
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<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>
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
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@ -352,7 +351,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span> ci_min <span class="op">=</span> <span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">CIP</span>, side <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> ci_max <span class="op">=</span> <span class="fu">rsi_confidence_interval</span><span class="op">(</span><span class="va">CIP</span>, side <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> <span class="op">)</span></span></span>
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<span class="r-in"><span> </span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ward cipro_R ci_min ci_max</span>
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@ -370,7 +368,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> <span class="va">resistance</span></span></span>
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<span class="r-in"><span> <span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
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<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
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@ -384,7 +381,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.290 0.400 0.662 1 0.086<span style="text-decoration: underline;">2</span> 0.089<span style="text-decoration: underline;">4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.2 0.368 0.605 <span style="color: #BB0000;">NA</span> 0.054<span style="text-decoration: underline;">1</span> 0.054<span style="text-decoration: underline;">1</span></span>
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<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>
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<span class="r-in"><span></span></span>
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<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>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
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