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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup
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dr. M.S. (Matthijs) Berends committed
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@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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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">1.3.0.9034</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
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@@ -296,17 +296,12 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<ul>
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<li><p>EUCAST Expert Rules. Version 2.0, 2012. <br />
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Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
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<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
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<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <br />
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<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
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<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <br />
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<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf</a></p></li>
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<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
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<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
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<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <br />
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<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx</a></p></li>
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<li><p>EUCAST Expert Rules. Version 2.0, 2012.<br />
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Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>(link)</a></p></li>
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<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>(link)</a></p></li>
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<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>(link)</a></p></li>
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<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
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<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
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</ul>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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@@ -333,7 +328,7 @@ 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 used 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'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine truncated
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<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine 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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