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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47
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dr. M.S. (Matthijs) Berends committed
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@@ -52,6 +52,9 @@
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<meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.
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To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details." />
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary_large_image" />
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<meta name="twitter:creator" content="@msberends" />
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<meta name="twitter:site" content="@univgroningen" />
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@@ -91,7 +94,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
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</span>
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</div>
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@@ -372,7 +375,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
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<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
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<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01MA02</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01MA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01MA08</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01MA16</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01MA15</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no'>J01MA11</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01MA12</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01MA07</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01MA14</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01MA06</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no'>J01MA01</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no'>J01MA18</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01MA03</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01MA17</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01MA10</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01MA09</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01MA05</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01MA13</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01CA01</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01CA04</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01CA12</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01CR05</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01CA13</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01AA02</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01FA10</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01FA09</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01CR02</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01AA08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01FA06</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01CF04</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01CF05</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01CR01</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01CE04</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01CA09</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DF01</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01CA06</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01CE08</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01CE10</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no'>J01CE0Line truncated
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<p>Amikacin (<code>AMK</code>, <a href='https://rdrr.io/r/base/NULL.html'>NULL</a>(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>c("J01MA12", "S01AE05")</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>c("J01CA01", "S01AA19")</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",'>J01CA04</a>&showdescription=no)), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CA12</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",'>J01CR05</a>&showdescription=no)), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA13</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>c("A01AB22", "J01AA02")</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>c("J01FA10", "S01AA26")</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",'>J01FA09</a>&showdescription=no)), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CR02</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>c("J01MA02", "S01AE03", "S02AA15", "S03AA07")</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>c("J01MA14", "S01AE07")</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>c("J01MA01", "S01AE01", "S02AA16")</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>c("A01AB23", "D10AF07", "J01AA08")</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01FA06</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no'>J01CF04</a>), ceftazidime (<code>CAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no'>J01CF05</a>), ceftriaxone (<code>CRO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no'>c("J01CE01", "S01AA14")</a>), cefuroxime (<code>CXM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",'>c("D06AX01", "D09AA02", "J01XC01", "S01AA13")</a>&showdescription=no)), cephalexin (<code>LEX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no'>J01FF02</a>), cephalothin (<code>CEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no'>J04AB02</a>), chloramphenicol (<code>CHL</code>, J01XX09(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (<code>CIP</code>, J01XX08(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (<code>CLR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no'>J01DB04</a>), clindamycin (<code>CLI</code>, J01DC01(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (<code>COL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",'>c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")</a>&showdescription=no)), daptomycin (<code>DAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no'>J01XE01</a>), doxycycline (<code>DOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",'>J01AA12</a>&showdescription=no)), epicillin (<code>EPC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no'>c("J01DC02", "S01AA27")</a>), ertapenem (<code>ETP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no'>c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")</a>), flucloxacillin (<code>FLC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no'>c("A07AA10", "J01XB01")</a>), fosfomycin (<code>FOS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no'>J01DD01</a>), fusidic acid (<code>FUS</code>, J01DD04(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (<code>GEN</code>, J01DF01(https://www.whocc.no/atc_ddd_indexLine truncated
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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