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2026-01-16 10:08:12 +00:00
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100 changed files with 264 additions and 236 deletions
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reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9018</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,9 +174,9 @@
<li><p><code><a href="antimicrobial_selectors.html">rifamycins()</a></code> can select: <br> rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine</p></li>
<li><p><code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> can select: <br> zoliflodacin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">streptogramins()</a></code> can select: <br> pristinamycin and quinupristin/dalfopristin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> can select: <br> brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea</p></li>
<li><p><code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> can select: <br> cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline</p></li>
<li><p><code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> can select: <br> brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> can select: <br> isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea, sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> can select: <br> cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, tetracycline/oleandomycin, and tigecycline</p></li>
<li><p><code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> can select: <br> brodimoprim, iclaprim, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> can select: <br> azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam</p></li>
</ul></div>
@@ -243,14 +243,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">esbl</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be tazobactam (TAZ)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">mecC</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be mecillinam (MEC)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanA</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be lenampicillin (LEN)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanB</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be metronidazole (MTR)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`cephalosporins_2nd()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (cefoxitin)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around </span><span style="color: #0000BB; background-color: #444444;">`all()`</span><span style="color: #0000BB;"> or</span></span>