Built site for AMR@3.0.1.9008: 9d1b456

reference/custom_mdro_guideline.html

@@ -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="">3.0.1.9009</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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">
@@ -70,7 +70,7 @@
 
 
 <dt id="arg-as-factor">as_factor<a class="anchor" aria-label="anchor" href="#arg-as-factor"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector. For combining rules sets (using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>) this value will be inherited from the first set at default.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdatatable.gitlab.io/data.table/reference/fctr.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector. For combining rules sets (using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>) this value will be inherited from the first set at default.</p></dd>
 
 
 <dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
@@ -144,8 +144,8 @@
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins_2nd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #2"</span>,</span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>      <span class="op">~</span> <span class="st">"My MDRO #3"</span></span>
 <span><span class="op">)</span></span></code></pre><p></p></div>
-<p>All 35 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <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><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin and ampicillin</p></li>
+<p>All 38 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <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><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, and ampicillin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <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><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <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, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">betalactams()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam</p></li>
@@ -160,17 +160,19 @@
 <li><p><code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> can select: <br> besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> can select: <br> cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test</p></li>
-<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, lincomycin, and pirlimycin</p></li>
+<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> can select: <br> dalbavancin, oritavancin, and telavancin</p></li>
-<li><p><code><a href="antimicrobial_selectors.html">macrolides()</a></code> can select: <br> acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin</p></li>
+<li><p><code><a href="antimicrobial_selectors.html">macrolides()</a></code> can select: <br> acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">monobactams()</a></code> can select: <br> aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> can select: <br> furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> can select: <br> cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">penicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">phenicols()</a></code> can select: <br> chloramphenicol, florfenicol, and thiamphenicol</p></li>
+<li><p><code><a href="antimicrobial_selectors.html">phosphonics()</a></code> can select: <br> amikacin/fosfomycin and fosfomycin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">polymyxins()</a></code> can select: <br> colistin, polymyxin B, and polymyxin B/polysorbate 80</p></li>
-<li><p><code><a href="antimicrobial_selectors.html">quinolones()</a></code> can select: <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><code><a href="antimicrobial_selectors.html">quinolones()</a></code> can select: <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, ozenoxacin, 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><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>