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@@ -9,7 +9,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9033</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9034</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -177,34 +177,18 @@
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<p>According to previously-mentioned sources, there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).</p>
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<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table></div>
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<div class="section">
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<h3 id="isolate-based">Isolate-based<a class="anchor" aria-label="anchor" href="#isolate-based"></a></h3>
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<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table><p><strong>Isolate-based</strong></p>
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<p><em>Minimum variables required: Microorganism identifier</em></p>
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<p>This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>
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</div>
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<div class="section">
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<h3 id="patient-based">Patient-based<a class="anchor" aria-label="anchor" href="#patient-based"></a></h3>
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<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>
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</div>
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<div class="section">
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<h3 id="episode-based">Episode-based<a class="anchor" aria-label="anchor" href="#episode-based"></a></h3>
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<p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.</p>
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<p><strong>Patient-based</strong></p>
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<p><em>Minimum variables required: Microorganism identifier, Patient identifier</em></p>
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<p>This method includes every genus-species combination per patient once. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>
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<p><strong>Episode-based</strong></p>
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<p><em>Minimum variables required: Microorganism identifier, Patient identifier, Date</em></p>
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<p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be e.g., 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.</p>
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<p>This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolate cannot be differentiated from a wildtype <em>Staphylococcus aureus</em> isolate.</p>
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</div>
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<div class="section">
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<h3 id="phenotype-based">Phenotype-based<a class="anchor" aria-label="anchor" href="#phenotype-based"></a></h3>
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<p><strong>Phenotype-based</strong></p>
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<p><em>Minimum variables required: Microorganism identifier, Patient identifier, Date, Antimicrobial test results</em></p>
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<p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol><li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code> (default)</p>
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<p>This method weighs <em>all</em> antimicrobial drugs available in the data set. Any difference from I to S or R (or vice versa) counts as <code>0.5</code> points, a difference from S to R (or vice versa) counts as <code>1</code> point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be selected as a first weighted isolate.</p>
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<p>All antimicrobials are internally selected using the <code><a href="key_antimicrobials.html">all_antimicrobials()</a></code> function. The output of this function does not need to be passed to the <code>first_isolate()</code> function.</p></li>
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@@ -227,26 +211,26 @@
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; font-weight: bold;">365 days</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_date`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_date`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;"> of 2</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;">=> Found </span><span style="color: #080808; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #080808;"> (69.4% of total where a</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> microbial ID was available)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (69.4% of total where a</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
@@ -257,20 +241,20 @@
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_is_gram_negative()`</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #444444;">`mo_is_gram_negative()`</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 441 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical <span style="color: #949494;">B_</span>PSDMN<span style="color: #949494;">_</span>AERG <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU <span style="color: #949494;">B_</span>SERRT<span style="color: #949494;">_</span>MRCS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895 85 F Clinical <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193 69 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical <span style="color: #949494;">B_</span>PSDMN<span style="color: #949494;">_</span>AERG <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 431 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
@@ -288,21 +272,21 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;"> of 2</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;">=> Found </span><span style="color: #080808; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #080808;"> (69.4% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">1,387 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (69.4% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
@@ -318,16 +302,16 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,387 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-17 495616 67 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-19 738003 71 M Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-21 462081 75 F Clinical <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-22 F35553 50 M ICU <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-03 481442 76 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1,377 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
@@ -348,18 +332,18 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "Clinical"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Excluding 9 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;">=> Found </span><span style="color: #080808; font-weight: bold;">865 'phenotype-based' first isolates</span><span style="color: #080808;"> (70.1% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">865 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (70.1% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "ICU"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Excluding 6 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;">=> Found </span><span style="color: #080808; font-weight: bold;">452 'phenotype-based' first isolates</span><span style="color: #080808;"> (70.0% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">452 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (70.0% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">Group: ward = "Outpatient"</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">ℹ Excluding 1 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;">=> Found </span><span style="color: #080808; font-weight: bold;">99 'phenotype-based' first isolates</span><span style="color: #080808;"> (82.5% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #080808;"> microbial ID was available)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;">=> Found </span><span style="color: #BBBBBB; font-weight: bold;">99 'phenotype-based' first isolates</span><span style="color: #BBBBBB;"> (82.5% of total where a</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BBBBBB;"> microbial ID was available)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient mo first</span>
|
||||
|
||||
Reference in New Issue
Block a user