mirror of
https://github.com/msberends/AMR.git
synced 2025-07-19 17:43:22 +02:00
Built site for AMR: 1.8.1.9045@e7af5fc
This commit is contained in:
github-actions
@ -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="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
|
||||
@ -260,11 +260,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 804</span>
|
||||
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_all</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"># counts "S", "I" and "R"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
|
||||
@ -304,62 +304,62 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># \donttest{</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">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>R <span class="op">=</span> <span class="fu">count_R</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> I <span class="op">=</span> <span class="fu">count_I</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> S <span class="op">=</span> <span class="fu">count_S</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu">count_all</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>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu">n_rsi</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>
|
||||
<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>
|
||||
<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> R <span class="op">=</span> <span class="fu">count_R</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> I <span class="op">=</span> <span class="fu">count_I</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> S <span class="op">=</span> <span class="fu">count_S</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu">count_all</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>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu">n_rsi</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>
|
||||
<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>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Number of available isolates for a whole antibiotic class</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># (i.e., in this data set columns GEN, TOB, AMK, KAN)</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/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 class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</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="va">n_rsi</span><span class="op">)</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"># Count co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span> <span class="co"># Please mind that `susceptibility()` calculates percentages right away instead.</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 class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1433</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 class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1879</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 class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1879</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 class="fu">count_susceptible</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1399</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 class="fu">count_all</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1855</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 class="fu">count_all</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1855</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 class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1764</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 class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1936</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 class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1936</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Get number of S+I vs. R immediately of selected 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">count_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="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">count_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-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital_id antibiotic interpretation value</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A AMX SI 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A AMX R 108</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 A CIP SI 181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A CIP R 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B AMX SI 170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B AMX R 271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B CIP SI 414</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B CIP R 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 C AMX SI 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 C AMX R 110</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 C CIP SI 161</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 C CIP R 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 D AMX SI 241</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 D AMX R 315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 D CIP SI 425</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 D CIP R 76</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value</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;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 158</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 15</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user