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(v1.6.0.9010) big first_isolate() update

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dr. M.S. (Matthijs) Berends
2021-04-26 23:57:37 +02:00
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commit 93683a4ae2
38 changed files with 1134 additions and 933 deletions
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40
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@ -82,7 +82,7 @@
</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">1.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>
@ -242,7 +242,43 @@
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span></pre>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
<span class='fu'>key_antibiotics</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
universal_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>,
universal_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span><span class='op'>)</span>,
universal_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefuroxime"</span><span class='op'>)</span>,
universal_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"piperacillin/tazobactam"</span><span class='op'>)</span>,
universal_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ciprofloxacin"</span><span class='op'>)</span>,
universal_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span><span class='op'>)</span>,
GramPos_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"vancomycin"</span><span class='op'>)</span>,
GramPos_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"teicoplanin"</span><span class='op'>)</span>,
GramPos_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tetracycline"</span><span class='op'>)</span>,
GramPos_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"erythromycin"</span><span class='op'>)</span>,
GramPos_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"oxacillin"</span><span class='op'>)</span>,
GramPos_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"rifampin"</span><span class='op'>)</span>,
GramNeg_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"gentamicin"</span><span class='op'>)</span>,
GramNeg_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tobramycin"</span><span class='op'>)</span>,
GramNeg_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"colistin"</span><span class='op'>)</span>,
GramNeg_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefotaxime"</span><span class='op'>)</span>,
GramNeg_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ceftazidime"</span><span class='op'>)</span>,
GramNeg_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"meropenem"</span><span class='op'>)</span>,
warnings <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span>
<span class='va'>y</span>,
<span class='va'>z</span>,
type <span class='op'>=</span> <span class='st'>"keyantimicrobials"</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired Lifecycle</h2>

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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

2
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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

2
docs/reference/custom_eucast_rules.html
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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

106
docs/reference/first_isolate.html
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@ -82,7 +82,7 @@
</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">1.6.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>
@ -250,12 +250,13 @@
col_testcode <span class='op'>=</span> <span class='cn'>NULL</span>,
col_specimen <span class='op'>=</span> <span class='cn'>NULL</span>,
col_icu <span class='op'>=</span> <span class='cn'>NULL</span>,
col_keyantibiotics <span class='op'>=</span> <span class='cn'>NULL</span>,
col_keyantimicrobials <span class='op'>=</span> <span class='cn'>NULL</span>,
episode_days <span class='op'>=</span> <span class='fl'>365</span>,
testcodes_exclude <span class='op'>=</span> <span class='cn'>NULL</span>,
icu_exclude <span class='op'>=</span> <span class='cn'>FALSE</span>,
specimen_group <span class='op'>=</span> <span class='cn'>NULL</span>,
type <span class='op'>=</span> <span class='st'>"keyantibiotics"</span>,
type <span class='op'>=</span> <span class='st'>"points"</span>,
method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenotype-based"</span>, <span class='st'>"episode-based"</span>, <span class='st'>"patient-based"</span>, <span class='st'>"isolate-based"</span><span class='op'>)</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
@ -269,6 +270,7 @@
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
method <span class='op'>=</span> <span class='st'>"episode-based"</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@ -277,7 +279,7 @@
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
col_keyantibiotics <span class='op'>=</span> <span class='cn'>NULL</span>,
method <span class='op'>=</span> <span class='st'>"phenotype-based"</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
@ -313,8 +315,8 @@
<td><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU)</p></td>
</tr>
<tr>
<th>col_keyantibiotics</th>
<td><p>column name of the key antibiotics to determine first (weighted) isolates, see <code><a href='key_antibiotics.html'>key_antibiotics()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use <code>col_keyantibiotics = FALSE</code> to prevent this. Can also be the output of <code><a href='key_antibiotics.html'>key_antibiotics()</a></code>.</p></td>
<th>col_keyantimicrobials</th>
<td><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first (weighted) isolates, see <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code>.</p></td>
</tr>
<tr>
<th>episode_days</th>
@ -334,15 +336,19 @@
</tr>
<tr>
<th>type</th>
<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see <em>Details</em></p></td>
<td><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>method</th>
<td><p>the algorithm to apply, either <code>"phenotype-based"</code>, <code>"episode-based"</code>, <code>"patient-based"</code> or <code>"isolate-based"</code> (can be abbreviated), see <em>Details</em></p></td>
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see <em>Details</em></p></td>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>points_threshold</th>
<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></td>
<td><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>info</th>
@ -358,7 +364,7 @@
</tr>
<tr>
<th>...</th>
<td><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or arguments passed on to <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> when using <code>filter_first_weighted_isolate()</code></p></td>
<td><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or arguments passed on to <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> otherwise (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>)</p></td>
</tr>
</table>
@ -371,42 +377,69 @@
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
<p>To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different algorithms can be used to do so, see below.</p>
<p>These functions are context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='get_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Why this is so Important</h3>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Different algorithms</h3>
<p>To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://pubmed.ncbi.nlm.nih.gov/17304462/'>(Hindler <em>et al.</em> 2007)</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><code>filter_*()</code> Shortcuts</h3>
<p>According to Hindler <em>et al.</em> (2007, doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
), there are different algorithms to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All algorithms select on a combination of the taxonomic genus and species (not subspecies).</p>
<p>All mentioned algorithms are covered in the <code>first_isolate()</code> function:</p><table class='table'>
<tr><td><strong>Algorithm</strong></td><td><strong>Function to apply</strong></td></tr>
<tr><td>Isolate-based</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>Patient-based</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>Episode-based</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>Phenotype-based</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>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates.</p>
<p>The function <code>filter_first_isolate()</code> is essentially equal to either:</p><pre> <span class='va'>x</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='va'>x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span><span class='op'>)</span>
</pre>
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='va'>x</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>only_weighted_firsts <span class='op'>=</span> <span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>,
col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span>, <span class='va'>...</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>only_weighted_firsts</span> <span class='op'>==</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='op'>-</span><span class='va'>only_weighted_firsts</span>, <span class='op'>-</span><span class='va'>keyab</span><span class='op'>)</span>
</pre>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Isolate-based</h4>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key Antibiotics</h2>
<p>This algorithm 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>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Patient-based</h4>
<p>There are two ways to determine whether isolates can be included as first weighted isolates which will give generally the same results:</p><ol>
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> function.</p></li>
<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this algorithm makes sure that no duplicate isolates are selected from the same patient.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Episode-based</h4>
<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, long episodes are common for analysing regional and national data.</p>
<p>This is the most common algorithm 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 algorithm, 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>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Phenotype-based</h4>
<p>This is a more reliable algorithm, 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></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
<p>This method weighs <em>all</em> antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 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>
<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>
<li><p>Using <code>type = "keyantimicrobials"</code> and argument <code>ignore_I</code></p>
<p>This method only weighs specific antimicrobial agents, called <em>key antimicrobials</em>. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S or R (or vice versa) will lead to this.</p>
<p>Key antimicrobials are internally selected using the <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> function, but can also be added manually as a variable to the data and set in the <code>col_keyantimicrobials</code> argument. Another option is to pass the output of the <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> function directly to the <code>col_keyantimicrobials</code> argument.</p></li>
</ol>
<p>The default algorithm is phenotype-based (using <code>type = "points"</code>) and episode-based (using <code>episode_days = 365</code>). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -421,14 +454,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics()</a></code></p></div>
<div class='dont-index'><p><code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='co'># \donttest{</span>
<span class='co'># faster way, only works in R 3.2 and later:</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
@ -466,7 +498,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is counted only once.</span>
<span class='co'># Gentamicin resistance in hospital D appears to be 3.7% higher than</span>
<span class='co'># Gentamicin resistance in hospital D appears to be 4.2% higher than</span>
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
<span class='op'>}</span>
<span class='co'># }</span>

8
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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">1.6.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>
@ -496,9 +496,9 @@
</tr><tr>
<td>
<p><code><a href="key_antibiotics.html">key_antibiotics()</a></code> <code><a href="key_antibiotics.html">key_antibiotics_equal()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
</td>
<td><p>Key Antibiotics for First (Weighted) Isolates</p></td>
<td><p>Deprecated Functions</p></td>
</tr><tr>
<td>
@ -667,7 +667,7 @@
<tr>
<td>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
</td>
<td><p>Deprecated Functions</p></td>
</tr>

157
docs/reference/key_antibiotics.html → docs/reference/key_antimicrobials.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Key Antibiotics for First (Weighted) Isolates — key_antibiotics • AMR (for R)</title>
<title>(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Key Antibiotics for First (Weighted) Isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates." />
<meta property="og:title" content="(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials" />
<meta property="og:description" content="These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see first_isolate()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</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">1.6.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>
@ -233,48 +233,39 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Key Antibiotics for First (Weighted) Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/key_antibiotics.R'><code>R/key_antibiotics.R</code></a></small>
<div class="hidden name"><code>key_antibiotics.Rd</code></div>
<h1>(Key) Antimicrobials for First Weighted Isolates</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/key_antimicrobials.R'><code>R/key_antimicrobials.R</code></a></small>
<div class="hidden name"><code>key_antimicrobials.Rd</code></div>
</div>
<div class="ref-description">
<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.</p>
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span><span class='op'>(</span>
<pre class="usage"><span class='fu'>key_antimicrobials</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
universal_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>,
universal_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span><span class='op'>)</span>,
universal_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefuroxime"</span><span class='op'>)</span>,
universal_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"piperacillin/tazobactam"</span><span class='op'>)</span>,
universal_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ciprofloxacin"</span><span class='op'>)</span>,
universal_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span><span class='op'>)</span>,
GramPos_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"vancomycin"</span><span class='op'>)</span>,
GramPos_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"teicoplanin"</span><span class='op'>)</span>,
GramPos_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tetracycline"</span><span class='op'>)</span>,
GramPos_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"erythromycin"</span><span class='op'>)</span>,
GramPos_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"oxacillin"</span><span class='op'>)</span>,
GramPos_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"rifampin"</span><span class='op'>)</span>,
GramNeg_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"gentamicin"</span><span class='op'>)</span>,
GramNeg_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tobramycin"</span><span class='op'>)</span>,
GramNeg_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"colistin"</span><span class='op'>)</span>,
GramNeg_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefotaxime"</span><span class='op'>)</span>,
GramNeg_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ceftazidime"</span><span class='op'>)</span>,
GramNeg_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"meropenem"</span><span class='op'>)</span>,
warnings <span class='op'>=</span> <span class='cn'>TRUE</span>,
universal <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"ampicillin"</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>, <span class='st'>"cefuroxime"</span>,
<span class='st'>"piperacillin/tazobactam"</span>, <span class='st'>"ciprofloxacin"</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span><span class='op'>)</span>,
gram_negative <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"gentamicin"</span>, <span class='st'>"tobramycin"</span>, <span class='st'>"colistin"</span>, <span class='st'>"cefotaxime"</span>,
<span class='st'>"ceftazidime"</span>, <span class='st'>"meropenem"</span><span class='op'>)</span>,
gram_positive <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"vancomycin"</span>, <span class='st'>"teicoplanin"</span>, <span class='st'>"tetracycline"</span>, <span class='st'>"erythromycin"</span>,
<span class='st'>"oxacillin"</span>, <span class='st'>"rifampin"</span><span class='op'>)</span>,
antifungal <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anidulafungin"</span>, <span class='st'>"caspofungin"</span>, <span class='st'>"fluconazole"</span>, <span class='st'>"miconazole"</span>,
<span class='st'>"nystatin"</span>, <span class='st'>"voriconazole"</span><span class='op'>)</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span>
<span class='fu'>all_antimicrobials</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>antimicrobials_equal</span><span class='op'>(</span>
<span class='va'>y</span>,
<span class='va'>z</span>,
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"points"</span>, <span class='st'>"keyantimicrobials"</span><span class='op'>)</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
@ -290,24 +281,24 @@
<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
</tr>
<tr>
<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
<th>universal</th>
<td><p>names of <strong>broad-spectrum</strong> antimicrobial agents, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></td>
</tr>
<tr>
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
<td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
<th>gram_negative</th>
<td><p>names of antibiotic agents for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></td>
</tr>
<tr>
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
<td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
<th>gram_positive</th>
<td><p>names of antibiotic agents for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></td>
</tr>
<tr>
<th>warnings</th>
<td><p>give a warning about missing antibiotic columns (they will be ignored)</p></td>
<th>antifungal</th>
<td><p>names of antifungal agents for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default agents.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other arguments passed on to functions</p></td>
<td><p>ignored, allows for future extensions</p></td>
</tr>
<tr>
<th>y, z</th>
@ -315,62 +306,63 @@
</tr>
<tr>
<th>type</th>
<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see <em>Details</em></p></td>
<td><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see <em>Details</em></p></td>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>points_threshold</th>
<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></td>
<td><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>info</th>
<td><p>unused - previously used to indicate whether a progress bar should print</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether comparison with <code>NA</code> should return <code>FALSE</code> (defaults to <code>TRUE</code> for backwards compatibility)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>key_antibiotics()</code> function is context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See <code><a href='first_isolate.html'>first_isolate()</a></code> for more info.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are:</p><ul>
<li><p>Amoxicillin</p></li>
<p>The <code>key_antimicrobials()</code> and <code>all_antimicrobials()</code> functions are context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
<p>The function <code>key_antimicrobials()</code> returns a character vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a character vector with all antimicrobial results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>Please see the <code><a href='first_isolate.html'>first_isolate()</a></code> function how these important functions enable the 'phenotype-based' method for determination of first isolates.</p>
<p>The default antimicrobial agents used for <strong>all rows</strong> (set in <code>universal</code>) are:</p><ul>
<li><p>Ampicillin</p></li>
<li><p>Amoxicillin/clavulanic acid</p></li>
<li><p>Cefuroxime</p></li>
<li><p>Piperacillin/tazobactam</p></li>
<li><p>Ciprofloxacin</p></li>
<li><p>Piperacillin/tazobactam</p></li>
<li><p>Trimethoprim/sulfamethoxazole</p></li>
<li><p>Vancomycin</p></li>
<li><p>Teicoplanin</p></li>
<li><p>Tetracycline</p></li>
</ul>
<p>The default antimicrobial agents used for <strong>Gram-negative bacteria</strong> (set in <code>gram_negative</code>) are:</p><ul>
<li><p>Cefotaxime</p></li>
<li><p>Ceftazidime</p></li>
<li><p>Colistin</p></li>
<li><p>Gentamicin</p></li>
<li><p>Meropenem</p></li>
<li><p>Tobramycin</p></li>
</ul>
<p>The default antimicrobial agents used for <strong>Gram-positive bacteria</strong> (set in <code>gram_positive</code>) are:</p><ul>
<li><p>Erythromycin</p></li>
<li><p>Oxacillin</p></li>
<li><p>Rifampin</p></li>
<li><p>Teicoplanin</p></li>
<li><p>Tetracycline</p></li>
<li><p>Vancomycin</p></li>
</ul>
<p>At default the antibiotics that are used for <strong>Gram-negative bacteria</strong> are:</p><ul>
<li><p>Amoxicillin</p></li>
<li><p>Amoxicillin/clavulanic acid</p></li>
<li><p>Cefuroxime</p></li>
<li><p>Piperacillin/tazobactam</p></li>
<li><p>Ciprofloxacin</p></li>
<li><p>Trimethoprim/sulfamethoxazole</p></li>
<li><p>Gentamicin</p></li>
<li><p>Tobramycin</p></li>
<li><p>Colistin</p></li>
<li><p>Cefotaxime</p></li>
<li><p>Ceftazidime</p></li>
<li><p>Meropenem</p></li>
<p>The default antimicrobial agents used for <strong>fungi</strong> (set in <code>antifungal</code>) are:</p><ul>
<li><p>Anidulafungin</p></li>
<li><p>Caspofungin</p></li>
<li><p>Fluconazole</p></li>
<li><p>Miconazole</p></li>
<li><p>Nystatin</p></li>
<li><p>Voriconazole</p></li>
</ul>
<p>The function <code>key_antibiotics_equal()</code> checks the characters returned by <code>key_antibiotics()</code> for equality, and returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -378,17 +370,6 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key Antibiotics</h2>
<p>There are two ways to determine whether isolates can be included as first weighted isolates which will give generally the same results:</p><ol>
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code>key_antibiotics()</code> function.</p></li>
<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>
<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>
@ -402,30 +383,30 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># output of the `key_antibiotics()` function could be like this:</span>
<span class='co'># output of the `key_antimicrobials()` function could be like this:</span>
<span class='va'>strainA</span> <span class='op'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='va'>strainB</span> <span class='op'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='co'># those strings can be compared with:</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span><span class='op'>)</span>
<span class='fu'>antimicrobials_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, type <span class='op'>=</span> <span class='st'>"keyantimicrobials"</span><span class='op'>)</span>
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, ignore_I <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>antimicrobials_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, type <span class='op'>=</span> <span class='st'>"keyantimicrobials"</span>, ignore_I <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># FALSE, because I is not ignored and so the 4th character differs</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># set key antibiotics to a new variable</span>
<span class='va'>my_patients</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'>key_antibiotics</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='co'># no need to define `x`</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'>key_antimicrobials</span><span class='op'>(</span>antifungal <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='co'># no need to define `x`</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>
<span class='co'># now calculate first isolates</span>
first_regular <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantibiotics <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
first_regular <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantimicrobials <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
<span class='co'># and first WEIGHTED isolates</span>
first_weighted <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span><span class='op'>)</span>
first_weighted <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantimicrobials <span class='op'>=</span> <span class='st'>"keyab"</span><span class='op'>)</span>
<span class='op'>)</span>
<span class='co'># Check the difference, in this data set it results in a lot more isolates:</span>
<span class='co'># Check the difference, in this data set it results in more isolates:</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_regular</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_weighted</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='op'>}</span>

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</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>

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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
</span>
</div>