P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 05:41:59 +02:00
Code Releases Activity

(v0.7.1.9005) new rsi calculations, atc class removal

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-07-01 14:03:15 +02:00
parent 65c6702b21
commit 156d550895
78 changed files with 1169 additions and 911 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/reference/AMR-deprecated.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/AMR.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/WHOCC.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/WHONET.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/ab_property.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/age.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/age_groups.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/antibiotics.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/as.ab.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/as.disk.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/as.mic.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

11
docs/reference/as.mo.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -322,12 +322,9 @@ This function uses intelligent rules to help getting fast and logical results. I
</ul><p>This means that looking up human pathogenic microorganisms takes less time than looking up human non-pathogenic microorganisms.</p>
<p><strong>Uncertain results</strong> <br />
The algorithm can additionally use three different levels of uncertainty to guess valid results. The default is <code>allow_uncertain = TRUE</code>, which is equal to uncertainty level 2. Using <code>allow_uncertain = FALSE</code> will skip all of these additional rules:</p><ul>
<li><p>(uncertainty level 1): It tries to look for only matching genera</p></li>
<li><p>(uncertainty level 1): It tries to look for previously accepted (but now invalid) taxonomic names</p></li>
<li><p>(uncertainty level 2): It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 2): It strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It strips off words from the start one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It tries any part of the name</p></li>
<li><p>(uncertainty level 1): It tries to look for only matching genera, previously accepted (but now invalid) taxonomic names and misspelled input</p></li>
<li><p>(uncertainty level 2): It removed parts between brackets, strips off words from the end one by one and re-evaluates the input with all previous rules</p></li>
<li><p>(uncertainty level 3): It strips off words from the start one by one and tries any part of the name</p></li>
</ul>
<p>You can also use e.g. <code>as.mo(..., allow_uncertain = 1)</code> to only allow up to level 1 uncertainty.</p>
<p>Examples:</p><ul>

7
docs/reference/as.rsi.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -303,15 +303,14 @@
<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>
<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>
<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>
<ul>
<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>
<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>
<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>
</ul>
<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>
<p>Source: <a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>.</p>
<p><strong>This AMR package honours this new insight.</strong></p>
<p>This AMR package honours this new insight. Use <code><a href='portion.html'>portion_SI</a></code> to determine antimicrobial susceptibility and <code><a href='count.html'>count_SI</a></code> to count susceptible isolates.</p>
<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>

2
docs/reference/atc_online.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/availability.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

85
docs/reference/count.html
View File

@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -243,19 +243,19 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</div>
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>)
<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>(),
<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>
@ -268,8 +268,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<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>
</tr>
<tr>
<th>also_single_tested</th>
<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>
<th>only_all_tested</th>
<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>
</tr>
<tr>
<th>data</th>
@ -311,15 +311,52 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<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>
<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>
<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>
<ul>
<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>
<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>
<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>
</ul>
<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>
<p>Source: <a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>.</p>
<p><strong>This AMR package honours this new insight.</strong></p>
<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>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
<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>
<pre>
-------------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
Antibiotic Antibiotic ----------------------- -----------------------
A B include as include as include as include as
numerator denominator numerator denominator
---------- ---------- ---------- ----------- ---------- -----------
S S X X X X
I S X X X X
R S X X X X
not tested S X X - -
S I X X X X
I I X X X X
R I X X X X
not tested I X X - -
S R X X X X
I R X X X X
R R - X - X
not tested R - - - -
S not tested X X - -
I not tested X X - -
R not tested - - - -
not tested not tested - - - -
-------------------------------------------------------------------------
</pre>
<p>Please note that for <code>only_all_tested = TRUE</code> applies that:</p><pre>
count_S() + count_I() + count_R() == count_all()
portion_S() + portion_I() + portion_R() == 1
</pre><p>and that for <code>only_all_tested = FALSE</code> applies that:</p><pre>
count_S() + count_I() + count_R() &gt;= count_all()
portion_S() + portion_I() + portion_R() &gt;= 1
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<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>
@ -351,8 +388,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<span class='co'># Since n_rsi counts available isolates, you can</span>
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
<span class='co'># This results in the same:</span>
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
<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>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@ -366,17 +403,17 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># S = 1342 (71.4%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
<span class='co'># Please mind that `portion_SI` calculates percentages right away instead.</span>
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># S = 1372 (74.0%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'>count_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># S = 1660 (92.3%)</span>
<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>
<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
<span class='fu'>count_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1764</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1936</span>
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@ -404,6 +441,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>

2
docs/reference/eucast_rules.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/extended-functions.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/filter_ab_class.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/first_isolate.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/freq.html
View File

@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/g.test.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/join.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/key_antibiotics.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/kurtosis.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/like.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/mdro.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/microorganisms.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/mo_source.html
View File

@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/p.symbol.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

115
docs/reference/portion.html
View File

@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -244,19 +244,19 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</div>
<pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_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>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@ -282,8 +282,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
</tr>
<tr>
<th>also_single_tested</th>
<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>
<th>only_all_tested</th>
<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>
</tr>
<tr>
<th>data</th>
@ -318,35 +318,60 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
<p>The function <code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each group and each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but adds the number of isolates.
<br /><br />
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
To calculate the probability (<em>p</em>) of susceptibility of more antibiotics (i.e. combination therapy), we need to check whether one of them has a susceptible result (as numerator) and count all cases where all antibiotics were tested (as denominator). <br />
<br />
For two antibiotics:
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
<br />
For three antibiotics:
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
<br />
And so on.</p>
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but adds the number of isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
<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>
<pre>
-------------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
Antibiotic Antibiotic ----------------------- -----------------------
A B include as include as include as include as
numerator denominator numerator denominator
---------- ---------- ---------- ----------- ---------- -----------
S S X X X X
I S X X X X
R S X X X X
not tested S X X - -
S I X X X X
I I X X X X
R I X X X X
not tested I X X - -
S R X X X X
I R X X X X
R R - X - X
not tested R - - - -
S not tested X X - -
I not tested X X - -
R not tested - - - -
not tested not tested - - - -
-------------------------------------------------------------------------
</pre>
<p>Please note that for <code>only_all_tested = TRUE</code> applies that:</p><pre>
count_S() + count_I() + count_R() == count_all()
portion_S() + portion_I() + portion_R() == 1
</pre><p>and that for <code>only_all_tested = FALSE</code> applies that:</p><pre>
count_S() + count_I() + count_R() &gt;= count_all()
portion_S() + portion_I() + portion_R() &gt;= 1
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<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>
<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>
<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>
<ul>
<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>
<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>
<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>
</ul>
<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>
<p>Source: <a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>.</p>
<p><strong>This AMR package honours this new insight.</strong></p>
<p>This AMR package honours this new insight. Use <code>portion_SI</code> to determine antimicrobial susceptibility and <code><a href='count.html'>count_SI</a></code> to count susceptible isolates.</p>
<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>
@ -380,7 +405,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>),
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
@ -394,32 +419,38 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>AMC</span>) <span class='co'># S = 71.4%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>) <span class='co'># %SI = 76.3%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>GEN</span>) <span class='co'># S = 74.0%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>GEN</span>) <span class='co'># %SI = 75.4%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># S = 92.3%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1798</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># %SI = 94.1%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1939</span>
<span class='co'># Using `also_single_tested` can be useful ...</span>
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>portion_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># S = 92.6%</span>
<span class='co'># ... but can also lead to selection bias - the data only has 2,000 rows:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_SI</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>portion</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
<span class='co'># numerator denominator portion</span>
<span class='co'># 1764 1936 0.9408</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># n = 2555</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_SI</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>portion</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='co'># numerator denominator portion</span>
<span class='co'># 1687 1798 0.9383</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>),
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_SI</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
@ -454,6 +485,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>

2
docs/reference/read.4D.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/resistance_predict.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/rsi_translation.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/septic_patients.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/skewness.html
View File

@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>