mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 11:48:00 +02:00
Built site for AMR@2.1.1.9227: d77ad6b
This commit is contained in:
github-actions
@ -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="">2.1.1.9224</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
|
||||
@ -105,7 +105,7 @@
|
||||
<span><span class="co">#> 1 Escherichia coli R S S</span></span>
|
||||
<span><span class="co">#> 2 Klebsiella pneumoniae R S S</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> mo TZP ampi cipro</span></span>
|
||||
<span><span class="co">#> 1 Escherichia coli R R S</span></span>
|
||||
<span><span class="co">#> 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
|
||||
@ -119,7 +119,7 @@
|
||||
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
|
||||
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">y</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">df</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">y</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> mo TZP ampi cipro</span></span>
|
||||
<span><span class="co">#> 1 Escherichia coli R S S</span></span>
|
||||
<span><span class="co">#> 2 Klebsiella pneumoniae R R S</span></span></code></pre><p></p></div>
|
||||
@ -137,7 +137,7 @@
|
||||
<span><span class="co">#></span></span>
|
||||
<span><span class="co">#> 1. If TZP is "R" then set to "R":</span></span>
|
||||
<span><span class="co">#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
|
||||
<p>These 34 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
|
||||
<p>These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
|
||||
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
|
||||
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
|
||||
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
|
||||
@ -167,6 +167,7 @@
|
||||
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
|
||||
<li><p>rifamycins<br>(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)</p></li>
|
||||
<li><p>streptogramins<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
|
||||
<li><p>sulfonamides<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>tetracyclines<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>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)</p></li>
|
||||
<li><p>trimethoprims<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>
|
||||
@ -184,7 +185,7 @@
|
||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> A set of custom EUCAST rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFAFAF;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
|
||||
@ -195,11 +196,20 @@
|
||||
<span class="r-in"><span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span></span>
|
||||
<span class="r-in"><span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span></span>
|
||||
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> overwrite <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 0 × 9</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 variables: row <int>, col <chr>, mo_fullname <chr>, old <sir>, new <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># rule <chr>, rule_group <chr>, rule_name <chr>, rule_source <chr></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 8 × 9</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> row col mo_fullname old new rule rule_group rule_name rule_source</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><int></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;"><ord></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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 33 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># combine rule sets</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
@ -209,13 +219,13 @@
|
||||
<span class="r-in"><span><span class="va">x2</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> A set of custom EUCAST rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFAFAF;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFAFAF;"> R </span>:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM),</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN),</span>
|
||||
|
||||
Reference in New Issue
Block a user