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(v0.7.1.9005) new rsi calculations, atc class removal
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
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</span>
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</div>
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@ -243,19 +243,19 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</div>
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<pre class="usage"><span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<pre class="usage"><span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_all</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_all</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>n_rsi</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>n_rsi</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
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<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
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@ -268,8 +268,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed.</p></td>
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</tr>
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<tr>
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<th>also_single_tested</th>
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<td><p>a logical to indicate whether for combination therapies also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This could lead to selection bias.</strong></p></td>
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<th>only_all_tested</th>
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<td><p>(for combination therapies, i.e. using more than one variable for <code>...</code>) a logical to indicate that isolates must be tested for all antibiotics, see section <em>Combination therapy</em> below</p></td>
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</tr>
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<tr>
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<th>data</th>
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@ -311,15 +311,52 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
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<p>In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below. Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p>
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<p>In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p>
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<ul>
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<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
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<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
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<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
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</ul>
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<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
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<p>Source: <a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>.</p>
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<p><strong>This AMR package honours this new insight.</strong></p>
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<p>This AMR package honours this new insight. Use <code><a href='portion.html'>portion_SI</a></code> to determine antimicrobial susceptibility and <code>count_SI</code> to count susceptible isolates.</p>
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<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
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<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>portion_SI</code> works to calculate the %SI:</p>
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<pre>
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-------------------------------------------------------------------------
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only_all_tested = FALSE only_all_tested = TRUE
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Antibiotic Antibiotic ----------------------- -----------------------
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A B include as include as include as include as
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numerator denominator numerator denominator
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---------- ---------- ---------- ----------- ---------- -----------
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S S X X X X
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I S X X X X
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R S X X X X
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not tested S X X - -
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S I X X X X
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I I X X X X
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R I X X X X
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not tested I X X - -
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S R X X X X
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I R X X X X
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R R - X - X
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not tested R - - - -
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S not tested X X - -
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I not tested X X - -
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R not tested - - - -
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not tested not tested - - - -
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-------------------------------------------------------------------------
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</pre>
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<p>Please note that for <code>only_all_tested = TRUE</code> applies that:</p><pre>
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count_S() + count_I() + count_R() == count_all()
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portion_S() + portion_I() + portion_R() == 1
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</pre><p>and that for <code>only_all_tested = FALSE</code> applies that:</p><pre>
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count_S() + count_I() + count_R() >= count_all()
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portion_S() + portion_I() + portion_R() >= 1
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</pre>
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<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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@ -351,8 +388,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<span class='co'># Since n_rsi counts available isolates, you can</span>
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<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
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<span class='co'># This results in the same:</span>
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'><a href='portion.html'>portion_SI</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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@ -366,17 +403,17 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
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<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># S = 1342 (71.4%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
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<span class='co'># Please mind that `portion_SI` calculates percentages right away instead.</span>
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1433</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1879</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># S = 1372 (74.0%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1399</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1855</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
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<span class='fu'>count_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># S = 1660 (92.3%)</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1798</span>
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<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
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<span class='fu'>count_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1764</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
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<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1936</span>
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<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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@ -404,6 +441,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
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<li><a href="#combination-therapy">Combination therapy</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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