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Built site for AMR: 1.8.1.9045@e7af5fc
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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="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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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@@ -278,7 +278,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</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="co"># base R ------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># determines %R</span></span></span>
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<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># determines %R</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5955556</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 class="co"># determines %S+I</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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@@ -299,80 +299,88 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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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 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">hospital_id</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>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 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="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="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">hospital_id</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>R <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> SI <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
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<span class="r-in"><span> n2 <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 class="co"># same - analogous to n_distinct</span></span></span>
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<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># NOT the number of tested isolates!</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="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>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> SI <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
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<span class="r-in"><span> n2 <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 class="co"># same - analogous to n_distinct</span></span></span>
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<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="op">)</span> <span class="co"># NOT the number of tested isolates!</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="co"># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
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<span class="r-in"><span> <span class="co"># so we can see that combination therapy does a lot more than mono therapy:</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 class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># %SI = 76.3%</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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># n = 1879</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 class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 75.4%</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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1855</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 class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># %SI = 76.3%</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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># n = 1879</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 class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 75.4%</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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1855</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 class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 94.1%</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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1939</span></span></span>
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<span class="r-in"><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 class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1939</span></span></span>
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<span class="r-in"><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="co"># See Details on how `only_all_tested` works. Example:</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/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</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="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> numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</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="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/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</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></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>
|
||||
<span class="r-in"><span> numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><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>
|
||||
<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">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<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>cipro_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> cipro_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</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"><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>
|
||||
<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>
|
||||
<span class="r-in"><span> cipro_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> cipro_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Get proportions S/I/R immediately of all rsi columns</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>
|
||||
<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="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">proportion_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># It also supports grouping variables</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># (use rsi_df to also include the count)</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>
|
||||
<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="va">hospital_id</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<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">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<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="va">ward</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span> <span class="fu">rsi_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</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> hospital_id antibiotic interpretation value isolates</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A AMX SI 0.3932584 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A AMX R 0.6067416 108</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 A CIP SI 0.8743961 181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A CIP R 0.1256039 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B AMX SI 0.3854875 170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B AMX R 0.6145125 271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B CIP SI 0.8296593 414</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B CIP R 0.1703407 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 C AMX SI 0.3714286 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 C AMX R 0.6285714 110</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 C CIP SI 0.7970297 161</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 C CIP R 0.2029703 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 D AMX SI 0.4334532 241</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 D AMX R 0.5665468 315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 D CIP SI 0.8483034 425</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 D CIP R 0.1516966 76</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value isolates</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><ord></span> <span style="color: #949494; font-style: italic;"><dbl></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 AMX SI 0.423 357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 0.577 487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 0.853 741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 0.147 128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 0.369 158</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 0.631 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 0.810 362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 0.190 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 0.397 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 0.603 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 0.839 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 0.161 15</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user