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(v1.7.1.9070) Better WHONET support
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dr. M.S. (Matthijs) Berends committed
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@@ -17,7 +17,7 @@
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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="Released version">1.7.1.9068</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
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@@ -297,7 +297,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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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><a href="eucast_rules.html">eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://www.whocc.no/atc/structure_and_principles/" class="external-link">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" class="external-link">S01AE08</a>), amoxicillin (<code>AMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" class="external-link">J01MA02</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no" class="external-link">J01MA23</a>), ampicillin (<code>AMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no" class="external-link">J01MA04</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no" class="external-link">J01MA08</a>), arbekacin (<code>ARB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no" class="external-link">J01MA19</a>), aspoxicillin (<code>APX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no" class="external-link">J01MA16</a>), azidocillin (<code>AZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no" class="external-link">J01MA15</a>), azithromycin (<code>AZM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no" class="external-link">J01MA11</a>), azlocillin (<code>AZL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no" class="external-link">J01MA12</a>), aztreonam (<code>ATM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no" class="external-link">J01MA24</a>), bacampicillin (<code>BAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no" class="external-link">J01MA07</a>), bekanamycin (<code>BEK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no" class="external-link">J01MA14</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no" class="external-link">D10AF05</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no" class="external-link">J01MA06</a>), benzylpenicillin (<code>PEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no" class="external-link">J01MA01</a>), besifloxacin (<code>BES</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no" class="external-link">J01MA18</a>), biapenem (<code>BIA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no" class="external-link">J01MA03</a>), carbenicillin (<code>CRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no" class="external-link">J01MA17</a>), carindacillin (<code>CRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no" class="external-link">J01MA10</a>), cefacetrile (<code>CAC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no" class="external-link">J01MA21</a>), cefaclor (<code>CEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no" class="external-link">J01MA09</a>), cefadroxil (<code>CFR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no" class="external-link">J01MA05</a>), cefaloridine (<code>RID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no" class="external-link">P01AA05</a>), cefamandole (<code>MAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no" class="external-link">J01MA22</a>), cefatrizine (<code>CTZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no" class="external-link">J01MA13</a>), cefazedone (<code>CZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no" class="external-link">J01CA01</a>), cefazolin (<code>CZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no" class="external-link">J01CA04</a>), cefcapene (<code>CCP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no" class="external-link">J01CA12</a>), cefdinir (<code>CDR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no" class="external-link">J01CR05</a>), cefditoren (<code>DIT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no" class="external-link">J01CA13</a>), cefepime (<code>FEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no" class="external-link">J01AA02</a>), cefetamet (<code>CAT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no" class="external-link">J01FA10</a>), cefixime (<code>CFM</code>, <aLine truncated
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<p>Amikacin (<code>AMK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no" class="external-link">S01AE08</a>), amoxicillin (<code>AMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" class="external-link">J01MA02</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no" class="external-link">J01MA23</a>), ampicillin (<code>AMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no" class="external-link">J01MA04</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no" class="external-link">J01MA08</a>), arbekacin (<code>ARB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no" class="external-link">J01MA19</a>), aspoxicillin (<code>APX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no" class="external-link">J01MA16</a>), azidocillin (<code>AZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no" class="external-link">J01MA15</a>), azithromycin (<code>AZM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no" class="external-link">J01MA11</a>), azlocillin (<code>AZL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no" class="external-link">J01MA12</a>), aztreonam (<code>ATM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no" class="external-link">J01MA24</a>), bacampicillin (<code>BAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no" class="external-link">J01MA07</a>), bekanamycin (<code>BEK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no" class="external-link">J01MA14</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no" class="external-link">D10AF05</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no" class="external-link">J01MA06</a>), benzylpenicillin (<code>PEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no" class="external-link">J01MA01</a>), besifloxacin (<code>BES</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no" class="external-link">J01MA18</a>), biapenem (<code>BIA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no" class="external-link">J01MA03</a>), carbenicillin (<code>CRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no" class="external-link">J01MA17</a>), carindacillin (<code>CRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no" class="external-link">J01MA10</a>), cefacetrile (<code>CAC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no" class="external-link">J01MA21</a>), cefaclor (<code>CEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no" class="external-link">J01MA09</a>), cefadroxil (<code>CFR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no" class="external-link">J01MA05</a>), cefaloridine (<code>RID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no" class="external-link">P01AA05</a>), cefamandole (<code>MAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no" class="external-link">J01MA22</a>), cefatrizine (<code>CTZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no" class="external-link">J01MA13</a>), cefazedone (<code>CZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no" class="external-link">J01CA01</a>), cefazolin (<code>CZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no" class="external-link">J01CA04</a>), cefcapene (<code>CCP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no" class="external-link">J01CA12</a>), cefdinir (<code>CDR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no" class="external-link">J01CR05</a>), cefditoren (<code>DIT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no" class="external-link">J01CA13</a>), cefepime (<code>FEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no" class="external-link">J01AA02</a>), cefetamet (<code>CAT</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no" class="external-link">J01FA10</a>), cefixime (<code>CFM</code>, <aLine truncated
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</div>
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<div id="interpretation-of-r-and-s-i">
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<h2>Interpretation of R and S/I</h2>
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